Merge pull request #209 from danilodileo/fix-warnings

Fix warnings
nf-core · Nov 27, 2023 · f7a3c45 · f7a3c45
2 parents 98de7b2 + e2fb870
commit f7a3c45
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Showing 59 changed files with 339 additions and 309 deletions.
diff --git 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  = true
+    //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
@@ -7,122 +7,122 @@
                 "nf-core": {
                     "bbmap/align": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbnorm": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "bbmap/index": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "ae9d9ead3688639bfd8dda19aeafe96ef38f3e83",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "363a40e3af1f2dec0545379f4ede49c1fac089f1",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "hmmer/hmmsearch": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "seqtk/mergepe": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "seqtk/seq": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "spades": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "subread/featurecounts": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "transdecoder/longorf": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "transdecoder/predict": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     }
                 }
@@ -131,7 +131,7 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "7c8eeb2b37a6c6d3ffba0aef55ff60c8718c0ba6",
+                        "git_sha": "af41b722617a973f3c2c0f83a5f64095e4d87ca2",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {

diff --git 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/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
@@ -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

diff --git 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
@@ -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')
 

diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml
diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf
diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml
diff --git a/modules/nf-core/bbmap/bbduk/main.nf b/modules/nf-core/bbmap/bbduk/main.nf
diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml
diff --git a/modules/nf-core/bbmap/bbnorm/main.nf b/modules/nf-core/bbmap/bbnorm/main.nf
diff --git a/modules/nf-core/bbmap/index/environment.yml b/modules/nf-core/bbmap/index/environment.yml
diff --git a/modules/nf-core/bbmap/index/main.nf b/modules/nf-core/bbmap/index/main.nf
diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml
diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf