From f0e5998c7933a399d39fe76c8889fd98406afbdd Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Fri, 3 Nov 2023 13:45:40 +0100 Subject: [PATCH 1/8] updated modules --- modules.json | 154 ++++++++++++------ modules/nf-core/bbmap/align/environment.yml | 8 + modules/nf-core/bbmap/align/main.nf | 2 +- modules/nf-core/bbmap/bbduk/environment.yml | 6 + modules/nf-core/bbmap/bbduk/main.nf | 2 +- modules/nf-core/bbmap/bbnorm/environment.yml | 7 + modules/nf-core/bbmap/bbnorm/main.nf | 2 +- modules/nf-core/bbmap/index/environment.yml | 6 + modules/nf-core/bbmap/index/main.nf | 2 +- modules/nf-core/cat/cat/environment.yml | 6 + modules/nf-core/cat/cat/main.nf | 2 +- modules/nf-core/cat/fastq/environment.yml | 6 + modules/nf-core/cat/fastq/main.nf | 2 +- .../dumpsoftwareversions/environment.yml | 6 + .../custom/dumpsoftwareversions/main.nf | 2 +- modules/nf-core/fastqc/environment.yml | 6 + modules/nf-core/fastqc/main.nf | 2 +- .../nf-core/hmmer/hmmsearch/environment.yml | 6 + modules/nf-core/hmmer/hmmsearch/main.nf | 2 +- modules/nf-core/multiqc/environment.yml | 6 + modules/nf-core/multiqc/main.nf | 2 +- modules/nf-core/prodigal/environment.yml | 7 + modules/nf-core/prodigal/main.nf | 2 +- modules/nf-core/prokka/environment.yml | 6 + modules/nf-core/prokka/main.nf | 2 +- .../nf-core/samtools/flagstat/environment.yml | 6 + modules/nf-core/samtools/flagstat/main.nf | 2 +- .../nf-core/samtools/idxstats/environment.yml | 6 + modules/nf-core/samtools/idxstats/main.nf | 2 +- .../nf-core/samtools/index/environment.yml | 6 + modules/nf-core/samtools/index/main.nf | 2 +- modules/nf-core/samtools/sort/environment.yml | 6 + modules/nf-core/samtools/sort/main.nf | 2 +- .../nf-core/samtools/stats/environment.yml | 6 + modules/nf-core/samtools/stats/main.nf | 2 +- modules/nf-core/seqtk/mergepe/environment.yml | 6 + modules/nf-core/seqtk/mergepe/main.nf | 2 +- modules/nf-core/seqtk/seq/environment.yml | 6 + modules/nf-core/seqtk/seq/main.nf | 2 +- modules/nf-core/spades/environment.yml | 6 + modules/nf-core/spades/main.nf | 2 +- .../subread/featurecounts/environment.yml | 6 + modules/nf-core/subread/featurecounts/main.nf | 2 +- .../transdecoder/longorf/environment.yml | 6 + modules/nf-core/transdecoder/longorf/main.nf | 2 +- .../transdecoder/predict/environment.yml | 6 + modules/nf-core/transdecoder/predict/main.nf | 2 +- modules/nf-core/trimgalore/environment.yml | 6 + modules/nf-core/trimgalore/main.nf | 2 +- 49 files changed, 275 insertions(+), 75 deletions(-) create mode 100644 modules/nf-core/bbmap/align/environment.yml create mode 100644 modules/nf-core/bbmap/bbduk/environment.yml create mode 100644 modules/nf-core/bbmap/bbnorm/environment.yml create mode 100644 modules/nf-core/bbmap/index/environment.yml create mode 100644 modules/nf-core/cat/cat/environment.yml create mode 100644 modules/nf-core/cat/fastq/environment.yml create mode 100644 modules/nf-core/custom/dumpsoftwareversions/environment.yml create mode 100644 modules/nf-core/fastqc/environment.yml create mode 100644 modules/nf-core/hmmer/hmmsearch/environment.yml create mode 100644 modules/nf-core/multiqc/environment.yml create mode 100644 modules/nf-core/prodigal/environment.yml create mode 100644 modules/nf-core/prokka/environment.yml create mode 100644 modules/nf-core/samtools/flagstat/environment.yml create mode 100644 modules/nf-core/samtools/idxstats/environment.yml create mode 100644 modules/nf-core/samtools/index/environment.yml create mode 100644 modules/nf-core/samtools/sort/environment.yml create mode 100644 modules/nf-core/samtools/stats/environment.yml create mode 100644 modules/nf-core/seqtk/mergepe/environment.yml create mode 100644 modules/nf-core/seqtk/seq/environment.yml create mode 100644 modules/nf-core/spades/environment.yml create mode 100644 modules/nf-core/subread/featurecounts/environment.yml create mode 100644 modules/nf-core/transdecoder/longorf/environment.yml create mode 100644 modules/nf-core/transdecoder/predict/environment.yml create mode 100644 modules/nf-core/trimgalore/environment.yml diff --git a/modules.json b/modules.json index a1ffe878..9823cf21 100644 --- a/modules.json +++ b/modules.json @@ -7,123 +7,171 @@ "nf-core": { "bbmap/align": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "bbmap/bbduk": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "bbmap/bbnorm": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "bbmap/index": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", - "git_sha": "ae9d9ead3688639bfd8dda19aeafe96ef38f3e83", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", - "git_sha": "363a40e3af1f2dec0545379f4ede49c1fac089f1", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "hmmer/hmmsearch": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "prodigal": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "prokka": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["bam_stats_samtools"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["bam_stats_samtools"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["bam_sort_stats_samtools"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/sort": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["bam_sort_stats_samtools"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/stats": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["bam_stats_samtools"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "bam_stats_samtools" + ] }, "seqtk/mergepe": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "seqtk/seq": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "spades": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "subread/featurecounts": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "transdecoder/longorf": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "transdecoder/predict": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] }, "trimgalore": { "branch": "master", - "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["modules"] + "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "installed_by": [ + "modules" + ] } } }, @@ -132,15 +180,19 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "7c8eeb2b37a6c6d3ffba0aef55ff60c8718c0ba6", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "bam_stats_samtools": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml new file mode 100644 index 00000000..693af269 --- /dev/null +++ b/modules/nf-core/bbmap/align/environment.yml @@ -0,0 +1,8 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bbmap=39.01 + - bioconda::samtools=1.16.1 + - pigz=2.6 diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf index 1f30f0ad..e3fee17d 100644 --- a/modules/nf-core/bbmap/align/main.nf +++ b/modules/nf-core/bbmap/align/main.nf @@ -2,7 +2,7 @@ process BBMAP_ALIGN { tag "$meta.id" label 'process_medium' - conda "bioconda::bbmap=39.01 bioconda::samtools=1.16.1 pigz=2.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' : 'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }" diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml new file mode 100644 index 00000000..59bc4662 --- /dev/null +++ b/modules/nf-core/bbmap/bbduk/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf index 001e27d4..6453afc6 100644 --- a/modules/nf-core/bbmap/bbduk/main.nf +++ b/modules/nf-core/bbmap/bbduk/main.nf @@ -2,7 +2,7 @@ process BBMAP_BBDUK { tag "$meta.id" label 'process_medium' - conda "bioconda::bbmap=39.01" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0': 'biocontainers/bbmap:39.01--h5c4e2a8_0' }" diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml new file mode 100644 index 00000000..09f517f9 --- /dev/null +++ b/modules/nf-core/bbmap/bbnorm/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bbmap=39.01 + - pigz=2.6 diff --git a/modules/nf-core/bbmap/bbnorm/main.nf b/modules/nf-core/bbmap/bbnorm/main.nf index 9974bfb4..1cac93de 100644 --- a/modules/nf-core/bbmap/bbnorm/main.nf +++ b/modules/nf-core/bbmap/bbnorm/main.nf @@ -2,7 +2,7 @@ process BBMAP_BBNORM { tag "$meta.id" label 'process_medium' - conda "bioconda::bbmap=39.01 pigz=2.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0': 'biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:e8a286b2e789c091bac0a57302cdc78aa0112353-0' }" diff --git a/modules/nf-core/bbmap/index/environment.yml b/modules/nf-core/bbmap/index/environment.yml new file mode 100644 index 00000000..59bc4662 --- /dev/null +++ b/modules/nf-core/bbmap/index/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf index e399bb3f..c9b61e17 100644 --- a/modules/nf-core/bbmap/index/main.nf +++ b/modules/nf-core/bbmap/index/main.nf @@ -2,7 +2,7 @@ process BBMAP_INDEX { tag "$fasta" label 'process_long' - conda "bioconda::bbmap=39.01" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0': 'biocontainers/bbmap:39.01--h5c4e2a8_0' }" diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml new file mode 100644 index 00000000..cdad6baa --- /dev/null +++ b/modules/nf-core/cat/cat/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf index 9f062219..4264a92c 100644 --- a/modules/nf-core/cat/cat/main.nf +++ b/modules/nf-core/cat/cat/main.nf @@ -2,7 +2,7 @@ process CAT_CAT { tag "$meta.id" label 'process_low' - conda "conda-forge::pigz=2.3.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : 'biocontainers/pigz:2.3.4' }" diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml new file mode 100644 index 00000000..222b301f --- /dev/null +++ b/modules/nf-core/cat/fastq/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf index 5021e6fc..3d963784 100644 --- a/modules/nf-core/cat/fastq/main.nf +++ b/modules/nf-core/cat/fastq/main.nf @@ -2,7 +2,7 @@ process CAT_FASTQ { tag "$meta.id" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..7ca22161 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.15 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b1..e562259e 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,7 +2,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 00000000..f52a53a0 --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 67209f79..50e59f2b 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,7 +2,7 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.12.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" diff --git a/modules/nf-core/hmmer/hmmsearch/environment.yml b/modules/nf-core/hmmer/hmmsearch/environment.yml new file mode 100644 index 00000000..e4787ce5 --- /dev/null +++ b/modules/nf-core/hmmer/hmmsearch/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::hmmer=3.3.2 diff --git a/modules/nf-core/hmmer/hmmsearch/main.nf b/modules/nf-core/hmmer/hmmsearch/main.nf index d40292d6..ad3117c8 100644 --- a/modules/nf-core/hmmer/hmmsearch/main.nf +++ b/modules/nf-core/hmmer/hmmsearch/main.nf @@ -2,7 +2,7 @@ process HMMER_HMMSEARCH { tag "$meta.id" label 'process_medium' - conda "bioconda::hmmer=3.3.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' : 'biocontainers/hmmer:3.3.2--h1b792b2_1' }" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..9d0e6b20 --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 40a691eb..2bbc3983 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,7 +1,7 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" diff --git a/modules/nf-core/prodigal/environment.yml b/modules/nf-core/prodigal/environment.yml new file mode 100644 index 00000000..05ca3ba0 --- /dev/null +++ b/modules/nf-core/prodigal/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::prodigal=2.6.3 + - conda-forge::pigz=2.6 diff --git a/modules/nf-core/prodigal/main.nf b/modules/nf-core/prodigal/main.nf index 8cf87a6d..b7df4787 100644 --- a/modules/nf-core/prodigal/main.nf +++ b/modules/nf-core/prodigal/main.nf @@ -2,7 +2,7 @@ process PRODIGAL { tag "$meta.id" label 'process_single' - conda "bioconda::prodigal=2.6.3 conda-forge::pigz=2.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' : 'biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }" diff --git a/modules/nf-core/prokka/environment.yml b/modules/nf-core/prokka/environment.yml new file mode 100644 index 00000000..b59d6c32 --- /dev/null +++ b/modules/nf-core/prokka/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::prokka=1.14.6 diff --git a/modules/nf-core/prokka/main.nf b/modules/nf-core/prokka/main.nf index 60fbe232..3ebf60bd 100644 --- a/modules/nf-core/prokka/main.nf +++ b/modules/nf-core/prokka/main.nf @@ -2,7 +2,7 @@ process PROKKA { tag "$meta.id" label 'process_low' - conda "bioconda::prokka=1.14.6" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/prokka%3A1.14.6--pl5321hdfd78af_4' : 'biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }" diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml new file mode 100644 index 00000000..04c82f14 --- /dev/null +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index b75707ec..9dee35a5 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml new file mode 100644 index 00000000..04c82f14 --- /dev/null +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 83c7c34b..b22d0843 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_IDXSTATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml new file mode 100644 index 00000000..04c82f14 --- /dev/null +++ b/modules/nf-core/samtools/index/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4b..256bd7c4 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml new file mode 100644 index 00000000..04c82f14 --- /dev/null +++ b/modules/nf-core/samtools/sort/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 2b7753fd..60f0c634 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_SORT { tag "$meta.id" label 'process_medium' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml new file mode 100644 index 00000000..04c82f14 --- /dev/null +++ b/modules/nf-core/samtools/stats/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.17 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 4a2607de..07286ef4 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -2,7 +2,7 @@ process SAMTOOLS_STATS { tag "$meta.id" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : 'biocontainers/samtools:1.17--h00cdaf9_0' }" diff --git a/modules/nf-core/seqtk/mergepe/environment.yml b/modules/nf-core/seqtk/mergepe/environment.yml new file mode 100644 index 00000000..8860e9f3 --- /dev/null +++ b/modules/nf-core/seqtk/mergepe/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::seqtk=1.3 diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf index 6a4362e5..8a42428d 100644 --- a/modules/nf-core/seqtk/mergepe/main.nf +++ b/modules/nf-core/seqtk/mergepe/main.nf @@ -2,7 +2,7 @@ process SEQTK_MERGEPE { tag "$meta.id" label 'process_single' - conda "bioconda::seqtk=1.3" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : 'biocontainers/seqtk:1.3--h5bf99c6_3' }" diff --git a/modules/nf-core/seqtk/seq/environment.yml b/modules/nf-core/seqtk/seq/environment.yml new file mode 100644 index 00000000..7dda5cd7 --- /dev/null +++ b/modules/nf-core/seqtk/seq/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf index b4524854..af085f0d 100644 --- a/modules/nf-core/seqtk/seq/main.nf +++ b/modules/nf-core/seqtk/seq/main.nf @@ -2,7 +2,7 @@ process SEQTK_SEQ { tag "$meta.id" label 'process_single' - conda "bioconda::seqtk=1.4" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_1' : 'biocontainers/seqtk:1.4--he4a0461_1' }" diff --git a/modules/nf-core/spades/environment.yml b/modules/nf-core/spades/environment.yml new file mode 100644 index 00000000..92566a4a --- /dev/null +++ b/modules/nf-core/spades/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::spades=3.15.5 diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index e424a182..010525e9 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -2,7 +2,7 @@ process SPADES { tag "$meta.id" label 'process_high' - conda "bioconda::spades=3.15.5" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1' : 'biocontainers/spades:3.15.5--h95f258a_1' }" diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml new file mode 100644 index 00000000..962c477f --- /dev/null +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::subread=2.0.1 diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index a524b92f..20979962 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -2,7 +2,7 @@ process SUBREAD_FEATURECOUNTS { tag "$meta.id" label 'process_medium' - conda "bioconda::subread=2.0.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : 'biocontainers/subread:2.0.1--hed695b0_0' }" diff --git a/modules/nf-core/transdecoder/longorf/environment.yml b/modules/nf-core/transdecoder/longorf/environment.yml new file mode 100644 index 00000000..5c3f92f9 --- /dev/null +++ b/modules/nf-core/transdecoder/longorf/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::transdecoder=5.5.0 diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/nf-core/transdecoder/longorf/main.nf index fcba9c5d..19466443 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/nf-core/transdecoder/longorf/main.nf @@ -2,7 +2,7 @@ process TRANSDECODER_LONGORF { tag "$meta.id" label 'process_medium' - conda "bioconda::transdecoder=5.5.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4' : 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/transdecoder/predict/environment.yml b/modules/nf-core/transdecoder/predict/environment.yml new file mode 100644 index 00000000..5c3f92f9 --- /dev/null +++ b/modules/nf-core/transdecoder/predict/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::transdecoder=5.5.0 diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf index a5c13fda..7d56a79d 100644 --- a/modules/nf-core/transdecoder/predict/main.nf +++ b/modules/nf-core/transdecoder/predict/main.nf @@ -2,7 +2,7 @@ process TRANSDECODER_PREDICT { tag "$meta.id" label 'process_medium' - conda "bioconda::transdecoder=5.5.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4': 'quay.io/comp-bio-aging/transdecoder' }" diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml new file mode 100644 index 00000000..a53a29a0 --- /dev/null +++ b/modules/nf-core/trimgalore/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::trim-galore=0.6.7 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index dcb77ae7..24ead871 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -2,7 +2,7 @@ process TRIMGALORE { tag "$meta.id" label 'process_high' - conda "bioconda::trim-galore=0.6.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" From 02aad5b9ec7e7d7be02f7b559973993d40d01ec3 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Fri, 3 Nov 2023 13:58:19 +0100 Subject: [PATCH 2/8] removed 2 more warnings --- modules/local/formatspades.nf | 2 +- modules/local/hmmrank.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/formatspades.nf b/modules/local/formatspades.nf index 1287b55b..a857d897 100644 --- a/modules/local/formatspades.nf +++ b/modules/local/formatspades.nf @@ -2,7 +2,7 @@ process FORMATSPADES { tag "$meta.id" label 'process_low' - conda "bioconda::gzip=1.11" + conda "conda-forge::gzip=1.11" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gzip:1.11': 'biocontainers/gzip:1.11' }" diff --git a/modules/local/hmmrank.nf b/modules/local/hmmrank.nf index 349b1da9..971b3489 100644 --- a/modules/local/hmmrank.nf +++ b/modules/local/hmmrank.nf @@ -11,8 +11,8 @@ process HMMRANK { tuple val(meta), path(hmmtargsums) output: - path "*.hmmrank.tsv.gz", emit: hmmrank - path "versions.yml" , emit: versions + tuple val(meta), path("*.hmmrank.tsv.gz"), emit: hmmrank + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when From dc0d1f8777d85d9b1193f8a64ce993752fb6ac7a Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Fri, 3 Nov 2023 16:07:10 +0100 Subject: [PATCH 3/8] add full test --- conf/test_full.config | 12 ++++++------ modules.json | 2 +- .../custom/dumpsoftwareversions/environment.yml | 2 +- .../nf-core/custom/dumpsoftwareversions/main.nf | 4 ++-- .../dumpsoftwareversions/tests/main.nf.test.snap | 14 +++++++------- 5 files changed, 17 insertions(+), 17 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 66971052..17e581d2 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,15 +15,15 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet_full_test.csv' // Genome references genome = 'R64-1-1' // parameters - skip_eukulele = false - skip_eggnog = false - skip_kofamscan = false + skip_eukulele = false + skip_eggnog = false + skip_kofamscan = false + eukulele_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/gtdb_eukulele' + eggnog_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/eggnog' } diff --git a/modules.json b/modules.json index 9823cf21..28b4a7c7 100644 --- a/modules.json +++ b/modules.json @@ -49,7 +49,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", + "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f", "installed_by": [ "modules" ] diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index 7ca22161..9d0e6b20 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -3,4 +3,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.15 + - bioconda::multiqc=1.17 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index e562259e..7685b33c 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -4,8 +4,8 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.17--pyhdfd78af_0' : + 'biocontainers/multiqc:1.17--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap index 8713b921..4274ed57 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -3,25 +3,25 @@ "content": [ { "0": [ - "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" ], "1": [ - "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" ], "2": [ - "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + "versions.yml:md5,3843ac526e762117eedf8825b40683df" ], "mqc_yml": [ - "software_versions_mqc.yml:md5,ee4a1d028ad29987f9ac511f4668f17c" + "software_versions_mqc.yml:md5,2570f4ba271ad08357b0d3d32a9cf84d" ], "versions": [ - "versions.yml:md5,f47ebd22aba1dd987b7e5d5247b766c3" + "versions.yml:md5,3843ac526e762117eedf8825b40683df" ], "yml": [ - "software_versions.yml:md5,a027f820f30b8191a20ca16465daaf37" + "software_versions.yml:md5,1c851188476409cda5752ce971b20b58" ] } ], - "timestamp": "2023-10-11T17:10:02.930699" + "timestamp": "2023-11-03T14:43:22.157011" } } From 8bfb5a0a00cfa4bc98af02eaed6ce3ae9ba23965 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 13 Nov 2023 16:02:37 +0100 Subject: [PATCH 4/8] fixed-issue-204 --- modules/local/eggnog/sum.nf | 9 ++++----- modules/local/sum_kofamscan.nf | 10 ++++------ modules/local/sum_taxonomy.nf | 5 +++-- 3 files changed, 11 insertions(+), 13 deletions(-) diff --git a/modules/local/eggnog/sum.nf b/modules/local/eggnog/sum.nf index 741ea1bb..6da8dafe 100644 --- a/modules/local/eggnog/sum.nf +++ b/modules/local/eggnog/sum.nf @@ -40,13 +40,12 @@ process EGGNOG_SUM { map_df(~read_tsv(., show_col_types = FALSE)) %>% mutate(sample = as.character(sample)) - counts %>% select(1, 7) %>% - right_join(eggnog, by = 'orf') %>% + counts %>% + inner_join(eggnog, by = 'orf') %>% group_by(sample) %>% drop_na() %>% - count(orf) %>% - summarise( value = sum(n), .groups = 'drop') %>% - add_column(database = "eggnog", field = "n_orfs") %>% + summarise( value = sum(count), .groups = 'drop') %>% + add_column(database = "eggnog", field = "eggnog_n_counts") %>% relocate(value, .after = last_col()) %>% write_tsv('${meta.id}.eggnog_summary.tsv.gz') diff --git a/modules/local/sum_kofamscan.nf b/modules/local/sum_kofamscan.nf index ceef2de3..03cc73c1 100644 --- a/modules/local/sum_kofamscan.nf +++ b/modules/local/sum_kofamscan.nf @@ -44,13 +44,11 @@ process SUM_KOFAMSCAN { map_df(~read_tsv(., show_col_types = FALSE)) %>% mutate(sample = as.character(sample)) - counts %>% select(1, 7) %>% - right_join(kofams, by = 'orf') %>% + counts %>% + inner_join(kofams, by = 'orf') %>% group_by(sample) %>% - drop_na() %>% - count(orf) %>% - summarise( value = sum(n), .groups = 'drop') %>% - add_column(database = "kofamscan", field = "n_orfs") %>% + summarise(value = sum(count), .groups = 'drop') %>% + add_column(database = "kofamscan", field = "kofamscan_n_counts") %>% relocate(value, .after = last_col()) %>% write_tsv('${meta.id}.kofamscan_summary.tsv.gz') diff --git a/modules/local/sum_taxonomy.nf b/modules/local/sum_taxonomy.nf index 1edd97ab..459e71c1 100644 --- a/modules/local/sum_taxonomy.nf +++ b/modules/local/sum_taxonomy.nf @@ -38,8 +38,9 @@ process SUM_TAXONOMY { # Join the two and count the number of ORFs with assigned taxonomy counts %>% inner_join(taxonomy, by = 'orf') %>% - count(sample, name = 'value') %>% - mutate(database = "${db ?: 'userdb'}", field = "eukulele_n_orfs") %>% + group_by(sample) %>% + summarise(value = sum(count), .groups = 'drop') %>% + mutate(database = "${db ?: 'userdb'}", field = "eukulele_n_counts") %>% relocate(value, .after = last_col()) %>% write_tsv('${prefix}_summary.tsv.gz') From 14ecc3c6e36982b94d07b58feb6466ad53c30446 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 13 Nov 2023 16:05:58 +0100 Subject: [PATCH 5/8] prettier --- modules.json | 106 +++++++++++++-------------------------------------- 1 file changed, 27 insertions(+), 79 deletions(-) diff --git a/modules.json b/modules.json index 28b4a7c7..b4ccca97 100644 --- a/modules.json +++ b/modules.json @@ -8,170 +8,122 @@ "bbmap/align": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbduk": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbnorm": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/index": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hmmer/hmmsearch": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prodigal": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prokka": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/sort": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "seqtk/mergepe": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/seq": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spades": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "transdecoder/longorf": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "transdecoder/predict": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trimgalore": { "branch": "master", "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -180,19 +132,15 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "7c8eeb2b37a6c6d3ffba0aef55ff60c8718c0ba6", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] } } } } } -} \ No newline at end of file +} From 64438513d11167d38e51cefdfeacf5f2cbc5fa63 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 14 Nov 2023 10:07:01 +0100 Subject: [PATCH 6/8] modules update --- modules.json | 156 ++++++--- modules/nf-core/bbmap/align/environment.yml | 1 + modules/nf-core/bbmap/bbduk/environment.yml | 1 + modules/nf-core/bbmap/bbnorm/environment.yml | 1 + modules/nf-core/bbmap/index/environment.yml | 1 + modules/nf-core/cat/cat/environment.yml | 1 + modules/nf-core/cat/fastq/environment.yml | 1 + .../dumpsoftwareversions/environment.yml | 1 + modules/nf-core/fastqc/environment.yml | 1 + .../nf-core/hmmer/hmmsearch/environment.yml | 1 + modules/nf-core/multiqc/environment.yml | 1 + modules/nf-core/prodigal/environment.yml | 1 + modules/nf-core/prokka/environment.yml | 1 + .../nf-core/samtools/flagstat/environment.yml | 1 + .../nf-core/samtools/idxstats/environment.yml | 1 + .../nf-core/samtools/index/environment.yml | 1 + modules/nf-core/samtools/sort/environment.yml | 1 + .../nf-core/samtools/stats/environment.yml | 1 + modules/nf-core/seqtk/mergepe/environment.yml | 1 + modules/nf-core/seqtk/seq/environment.yml | 1 + modules/nf-core/spades/environment.yml | 1 + .../subread/featurecounts/environment.yml | 1 + .../transdecoder/longorf/environment.yml | 1 + .../transdecoder/predict/environment.yml | 1 + modules/nf-core/trimgalore/environment.yml | 1 + .../tests/main.nf.test | 14 +- .../tests/main.nf.test.snap | 302 +++++------------- .../bam_sort_stats_samtools/tests/tags.yml | 2 +- 28 files changed, 217 insertions(+), 281 deletions(-) diff --git a/modules.json b/modules.json index b4ccca97..c08b597f 100644 --- a/modules.json +++ b/modules.json @@ -7,123 +7,171 @@ "nf-core": { "bbmap/align": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "bbmap/bbduk": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "bbmap/bbnorm": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "bbmap/index": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "hmmer/hmmsearch": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "prodigal": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "prokka": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["bam_stats_samtools"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["bam_stats_samtools"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["bam_sort_stats_samtools"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/sort": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["bam_sort_stats_samtools"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/stats": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["bam_stats_samtools"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "bam_stats_samtools" + ] }, "seqtk/mergepe": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "seqtk/seq": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "spades": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "subread/featurecounts": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "transdecoder/longorf": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "transdecoder/predict": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] }, "trimgalore": { "branch": "master", - "git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a", - "installed_by": ["modules"] + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "installed_by": [ + "modules" + ] } } }, @@ -131,16 +179,20 @@ "nf-core": { "bam_sort_stats_samtools": { "branch": "master", - "git_sha": "7c8eeb2b37a6c6d3ffba0aef55ff60c8718c0ba6", - "installed_by": ["subworkflows"] + "git_sha": "af41b722617a973f3c2c0f83a5f64095e4d87ca2", + "installed_by": [ + "subworkflows" + ] }, "bam_stats_samtools": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml index 693af269..96c4c32c 100644 --- a/modules/nf-core/bbmap/align/environment.yml +++ b/modules/nf-core/bbmap/align/environment.yml @@ -1,3 +1,4 @@ +name: bbmap_align channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml index 59bc4662..1221474c 100644 --- a/modules/nf-core/bbmap/bbduk/environment.yml +++ b/modules/nf-core/bbmap/bbduk/environment.yml @@ -1,3 +1,4 @@ +name: bbmap_bbduk channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml index 09f517f9..8b97ffda 100644 --- a/modules/nf-core/bbmap/bbnorm/environment.yml +++ b/modules/nf-core/bbmap/bbnorm/environment.yml @@ -1,3 +1,4 @@ +name: bbmap_bbnorm channels: - conda-forge - bioconda diff --git a/modules/nf-core/bbmap/index/environment.yml b/modules/nf-core/bbmap/index/environment.yml index 59bc4662..515f8d21 100644 --- a/modules/nf-core/bbmap/index/environment.yml +++ b/modules/nf-core/bbmap/index/environment.yml @@ -1,3 +1,4 @@ +name: bbmap_index channels: - conda-forge - bioconda diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml index cdad6baa..17a04ef2 100644 --- a/modules/nf-core/cat/cat/environment.yml +++ b/modules/nf-core/cat/cat/environment.yml @@ -1,3 +1,4 @@ +name: cat_cat channels: - conda-forge - bioconda diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 222b301f..bff93add 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,3 +1,4 @@ +name: cat_fastq channels: - conda-forge - bioconda diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index 9d0e6b20..f0c63f69 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -1,3 +1,4 @@ +name: custom_dumpsoftwareversions channels: - conda-forge - bioconda diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index f52a53a0..1787b38a 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,3 +1,4 @@ +name: fastqc channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmsearch/environment.yml b/modules/nf-core/hmmer/hmmsearch/environment.yml index e4787ce5..89978984 100644 --- a/modules/nf-core/hmmer/hmmsearch/environment.yml +++ b/modules/nf-core/hmmer/hmmsearch/environment.yml @@ -1,3 +1,4 @@ +name: hmmer_hmmsearch channels: - conda-forge - bioconda diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 9d0e6b20..e5e14e83 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,3 +1,4 @@ +name: MultiQC channels: - conda-forge - bioconda diff --git a/modules/nf-core/prodigal/environment.yml b/modules/nf-core/prodigal/environment.yml index 05ca3ba0..85746534 100644 --- a/modules/nf-core/prodigal/environment.yml +++ b/modules/nf-core/prodigal/environment.yml @@ -1,3 +1,4 @@ +name: prodigal channels: - conda-forge - bioconda diff --git a/modules/nf-core/prokka/environment.yml b/modules/nf-core/prokka/environment.yml index b59d6c32..d7c44d5a 100644 --- a/modules/nf-core/prokka/environment.yml +++ b/modules/nf-core/prokka/environment.yml @@ -1,3 +1,4 @@ +name: prokka channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 04c82f14..22bdb5cf 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,3 +1,4 @@ +name: samtools_flagstat channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 04c82f14..89bd272f 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,3 +1,4 @@ +name: samtools_idxstats channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 04c82f14..3c6f95b2 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,3 +1,4 @@ +name: samtools_index channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 04c82f14..508659f0 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,3 +1,4 @@ +name: samtools_sort channels: - conda-forge - bioconda diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 04c82f14..ed4e8961 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,3 +1,4 @@ +name: samtools_stats channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/mergepe/environment.yml b/modules/nf-core/seqtk/mergepe/environment.yml index 8860e9f3..cefab216 100644 --- a/modules/nf-core/seqtk/mergepe/environment.yml +++ b/modules/nf-core/seqtk/mergepe/environment.yml @@ -1,3 +1,4 @@ +name: seqtk_mergepe channels: - conda-forge - bioconda diff --git a/modules/nf-core/seqtk/seq/environment.yml b/modules/nf-core/seqtk/seq/environment.yml index 7dda5cd7..78dc2c84 100644 --- a/modules/nf-core/seqtk/seq/environment.yml +++ b/modules/nf-core/seqtk/seq/environment.yml @@ -1,3 +1,4 @@ +name: seqtk_seq channels: - conda-forge - bioconda diff --git a/modules/nf-core/spades/environment.yml b/modules/nf-core/spades/environment.yml index 92566a4a..12315814 100644 --- a/modules/nf-core/spades/environment.yml +++ b/modules/nf-core/spades/environment.yml @@ -1,3 +1,4 @@ +name: spades channels: - conda-forge - bioconda diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 962c477f..ca19439d 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -1,3 +1,4 @@ +name: subread_featurecounts channels: - conda-forge - bioconda diff --git a/modules/nf-core/transdecoder/longorf/environment.yml b/modules/nf-core/transdecoder/longorf/environment.yml index 5c3f92f9..29a06d31 100644 --- a/modules/nf-core/transdecoder/longorf/environment.yml +++ b/modules/nf-core/transdecoder/longorf/environment.yml @@ -1,3 +1,4 @@ +name: transdecoder_longorf channels: - conda-forge - bioconda diff --git a/modules/nf-core/transdecoder/predict/environment.yml b/modules/nf-core/transdecoder/predict/environment.yml index 5c3f92f9..07efaa4f 100644 --- a/modules/nf-core/transdecoder/predict/environment.yml +++ b/modules/nf-core/transdecoder/predict/environment.yml @@ -1,3 +1,4 @@ +name: transdecoder_predict channels: - conda-forge - bioconda diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index a53a29a0..6cd0f51b 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -1,3 +1,4 @@ +name: trimgalore channels: - conda-forge - bioconda diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test index a8a13f2a..59b749d8 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test @@ -5,7 +5,9 @@ nextflow_workflow { workflow "BAM_SORT_STATS_SAMTOOLS" tag "subworkflows" tag "subworkflows_nfcore" + tag "subworkflows/bam_sort_stats_samtools" tag "bam_sort_stats_samtools" + tag "subworkflows/bam_stats_samtools" tag "bam_stats_samtools" tag "samtools" tag "samtools/index" @@ -35,7 +37,11 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, + { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, + { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_single_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_single_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_single_end_idxstats") } ) } } @@ -61,7 +67,11 @@ nextflow_workflow { then { assertAll( { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert workflow.out.bam.get(0).get(1) ==~ ".*.bam"}, + { assert workflow.out.bai.get(0).get(1) ==~ ".*.bai"}, + { assert snapshot(workflow.out.stats).match("test_bam_sort_stats_samtools_paired_end_stats") }, + { assert snapshot(workflow.out.flagstat).match("test_bam_sort_stats_samtools_paired_end_flagstats") }, + { assert snapshot(workflow.out.idxstats).match("test_bam_sort_stats_samtools_paired_end_idxstats") } ) } } diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index 50ffde60..6dafc3bc 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -1,236 +1,86 @@ { - "test_bam_sort_stats_samtools_single_end": { + "test_bam_sort_stats_samtools_paired_end_flagstats": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,2cf8fe8dbba3da7eb4fb251c79f428dc" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,002488588110dcee464e65f68c4726e8" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,796f45f791f06291b76329528fae0a54" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ] - ], - "6": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,002488588110dcee464e65f68c4726e8" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,2cf8fe8dbba3da7eb4fb251c79f428dc" - ] - ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,796f45f791f06291b76329528fae0a54" - ] - ], - "versions": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" ] - } + ] ], - "timestamp": "2023-10-18T09:34:31.989804787" + "timestamp": "2023-10-22T20:25:03.687121177" }, - "test_bam_sort_stats_samtools_paired_end": { + "test_bam_sort_stats_samtools_paired_end_idxstats": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,81adec7882577c0ad17962599acf7745" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,9e6427a796975290b1110c9d542ac79d" - ] - ], - "2": [ - - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,f3f0e5aad236aae678ac5361b529a664" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" - ] - ], - "6": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" - ], - "bai": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam.bai:md5,9e6427a796975290b1110c9d542ac79d" - ] - ], - "bam": [ - [ - { - "id": "test", - "single_end": false - }, - "test.bam:md5,81adec7882577c0ad17962599acf7745" - ] - ], - "csi": [ - - ], - "flagstat": [ - [ - { - "id": "test", - "single_end": false - }, - "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783" - ] - ], - "idxstats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" - ] - ], - "stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test.stats:md5,f3f0e5aad236aae678ac5361b529a664" - ] - ], - "versions": [ - "versions.yml:md5,176f12ceae81f76341e481988c799c15", - "versions.yml:md5,7beadfaf6b22ea0ae6e655b41447803f", - "versions.yml:md5,bfcdd8e2d5151a14dac15a9332d73d52", - "versions.yml:md5,dd8f44a9bfef10555ef1c8cc0267ff9c", - "versions.yml:md5,f2eb7aba102adae159006c9a443c301b" + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2" ] - } + ] ], - "timestamp": "2023-10-18T09:34:57.682759147" + "timestamp": "2023-10-22T20:25:03.709648916" + }, + "test_bam_sort_stats_samtools_single_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,796f45f791f06291b76329528fae0a54" + ] + ] + ], + "timestamp": "2023-10-22T20:25:58.398627806" + }, + "test_bam_sort_stats_samtools_paired_end_stats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.stats:md5,f3f0e5aad236aae678ac5361b529a664" + ] + ] + ], + "timestamp": "2023-10-22T20:25:03.644306159" + }, + "test_bam_sort_stats_samtools_single_end_idxstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.idxstats:md5,613e048487662c694aa4a2f73ca96a20" + ] + ] + ], + "timestamp": "2023-10-22T20:25:58.451364604" + }, + "test_bam_sort_stats_samtools_single_end_flagstats": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.flagstat:md5,2191911d72575a2358b08b1df64ccb53" + ] + ] + ], + "timestamp": "2023-10-22T20:25:58.416859285" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml index a8274109..30b69d6a 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/tags.yml @@ -1,2 +1,2 @@ -bam_sort_stats_samtools: +subworkflows/bam_sort_stats_samtools: - subworkflows/nf-core/bam_sort_stats_samtools/** From a0c435bc1636f48ed1000e3d6b49aa0a23efa1ff Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Tue, 14 Nov 2023 12:47:47 +0100 Subject: [PATCH 7/8] prettier --- modules.json | 106 +++++++++++++-------------------------------------- 1 file changed, 27 insertions(+), 79 deletions(-) diff --git a/modules.json b/modules.json index c08b597f..fde4b23b 100644 --- a/modules.json +++ b/modules.json @@ -8,170 +8,122 @@ "bbmap/align": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbduk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbnorm": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hmmer/hmmsearch": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prodigal": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prokka": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/sort": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "seqtk/mergepe": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/seq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spades": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "transdecoder/longorf": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "transdecoder/predict": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trimgalore": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -180,19 +132,15 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "af41b722617a973f3c2c0f83a5f64095e4d87ca2", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] } } } } } -} \ No newline at end of file +} From e2fb8709f0b1907f7210363e9c42247424716727 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 27 Nov 2023 10:48:16 +0100 Subject: [PATCH 8/8] resolved full test --- conf/test_full.config | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index 17e581d2..afe002fe 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -21,9 +21,9 @@ params { genome = 'R64-1-1' // parameters - skip_eukulele = false + //skip_eukulele = false skip_eggnog = false - skip_kofamscan = false - eukulele_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/gtdb_eukulele' - eggnog_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/eggnog' + skip_kofamscan = true + //eukulele_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/gtdb_eukulele/' + eggnog_dbpath = 's3://ngi-igenomes/test-data/metatdenovo/eggnog/' }