Merge pull request #218 from danilodileo/release

Last PR before the release
nf-core · Dec 7, 2023 · 5b77bcd · 5b77bcd
2 parents 163312a + 9160116
commit 5b77bcd
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Showing 23 changed files with 71 additions and 58 deletions.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,8 +1,8 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/releases/tag/2.5.1" target="_blank">nf-core/metatdenovo</a>
+  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/releases/tag/1.0.0" target="_blank">nf-core/metatdenovo</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/metatdenovo/2.5.1/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/metatdenovo/1.0.0/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-metatdenovo-methods-description":

diff --git a/modules.json b/modules.json
@@ -67,27 +67,27 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "63e817de8c617131447192ab2c4e70b4ed4071f7",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "5394565c5fe4c760e5b35977ec7607c62e81d1f8",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "seqtk/mergepe": {
@@ -131,12 +131,12 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "af41b722617a973f3c2c0f83a5f64095e4d87ca2",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "0da36ce43056d68253d3c422c7137223ac6d3c3a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_sort_stats_samtools"]
                     }
                 }

diff --git a/modules/local/eukulele/search.nf b/modules/local/eukulele/search.nf
@@ -4,8 +4,8 @@ process EUKULELE_SEARCH {
 
     conda "bioconda::eukulele=2.0.5"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/eukulele:2.0.5--pyh723bec7_0' :
-        'biocontainers/eukulele:2.0.5--pyh723bec7_0' }"
+        'https://depot.galaxyproject.org/singularity/eukulele:2.0.7--pyh78b79e7_0' :
+        'biocontainers/eukulele:2.0.7--pyh78b79e7_0' }"
 
     input:
     tuple val(meta), path(fasta), val(dbname), path(eukdb)

diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml
diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf
diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test b/modules/nf-core/samtools/flagstat/tests/main.nf.test
diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml
diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf
diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test b/modules/nf-core/samtools/idxstats/tests/main.nf.test
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml
diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test
diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test b/modules/nf-core/samtools/stats/tests/main.nf.test
diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap
diff --git a/nextflow.config b/nextflow.config
@@ -282,7 +282,7 @@ manifest {
     description     = """Assembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.5.1'
+    version        = '1.0.0'
 }
 
 // Load modules.config for DSL2 module specific options

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -24,8 +24,8 @@
                 },
                 "se_reads": {
                     "type": "boolean",
-                    "default": false,
-                    "description": "activate when using single end reads input"
+                    "description": "activate when using single end reads input",
+                    "fa_icon": "fas fa-long-arrow-alt-right"
                 },
                 "outdir": {
                     "type": "string",
@@ -510,7 +510,6 @@
                 "validate_params": {
                     "type": "boolean",
                     "description": "Boolean whether to validate parameters against the schema at runtime",
-                    "default": false,
                     "fa_icon": "fas fa-check-square",
                     "hidden": true
                 },

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