Merge pull request #377 from nf-core/linting_fix

Fixed linting
nf-core · Aug 19, 2024 · 54eccfa · 54eccfa
2 parents 6e01548 + 4ca5936
commit 54eccfa
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#332]](https://github.com/nf-core/smrnaseq/issues/332) by [[#361]](https://github.com/nf-core/smrnaseq/pull/361) - Fix documentation to use only single-end
 - [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), change conda-base to conda-forge channel
 - [[#350]](https://github.com/nf-core/smrnaseq/pull/350) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), set python version to 3.7 to fix pysam issue
-- [[#351]](https://github.com/nf-core/smrnaseq/issues/351) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/pull/364) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols
+- [[#351]](https://github.com/nf-core/smrnaseq/issues/351) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/pull/364) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols.
+- [[#369]](https://github.com/nf-core/smrnaseq/issues/369) - Fix [Linting](https://github.com/nf-core/smrnaseq/pull/377) - Fixed linting warnings and updated modules & subworkflows.
 - [[#374]](https://github.com/nf-core/smrnaseq/pull/374) - Fix [default tests](https://github.com/nf-core/smrnaseq/issues/375) so that they do not require additional profiles in CI. Change GitHub CI fail-fast strategy to false.
 - [[#371]](https://github.com/nf-core/smrnaseq/issues/371) - Fix [Plain test profile](https://github.com/nf-core/smrnaseq/pull/372) - Updated default protocol value to "custom".
 - [[#375](https://github.com/nf-core/smrnaseq/pull/375) - Test merging of [technical repeats](https://github.com/nf-core/smrnaseq/issues/212)

diff --git a/modules.json b/modules.json
@@ -7,62 +7,62 @@
                 "nf-core": {
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8",
+                        "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
+                        "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["fastq_fastqc_umitools_fastp"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
+                        "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["bam_sort_stats_samtools", "modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
                         "installed_by": ["bam_stats_samtools", "modules"]
                     },
                     "umicollapse": {
                         "branch": "master",
-                        "git_sha": "b97197968ac12dde2463fa54541f6350c46f2035",
+                        "git_sha": "18e452a645bd56d1a539f53c7656e3d2915246f7",
                         "installed_by": ["modules"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "d2c5e76f291379f3dd403e48e46ed7e6ba5da744",
+                        "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
                         "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
                     },
                     "untarfiles": {
@@ -76,17 +76,17 @@
                 "nf-core": {
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "4352dbdb09ec40db71e9b172b97a01dcf5622c26",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "cabcc0dadf8366aa7a9930066a7b3dd90d9825d5",
+                        "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nextflow_pipeline": {

diff --git a/modules/local/bowtie_map_mirna.nf b/modules/local/bowtie_map_mirna.nf
@@ -2,7 +2,7 @@ process BOWTIE_MAP_SEQ {
     tag "$meta.id"
     label 'process_medium'
 
-    conda 'bowtie=1.3.0 bioconda::samtools=1.13'
+    conda 'bowtie=1.3.0 bioconda::samtools=1.20'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' :
         'biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0' }"

diff --git a/modules/local/edger_qc.nf b/modules/local/edger_qc.nf
@@ -1,7 +1,7 @@
 process EDGER_QC {
     label 'process_medium'
 
-    conda 'bioconda::bioconductor-limma=3.58.1 bioconda::bioconductor-edger=4.0.2 conda-forge::r-data.table=1.14.10 conda-forge::r-gplots=3.1.3 conda-forge::r-statmod=1.5.0'
+    conda 'bioconda::bioconductor-limma=3.58.1 bioconda::bioconductor-edger=4.0.16 conda-forge::r-data.table=1.14.10 conda-forge::r-gplots=3.1.3 conda-forge::r-statmod=1.5.0'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0' :
         'biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0' }"

diff --git a/modules/local/mirdeep2_mapper.nf b/modules/local/mirdeep2_mapper.nf
@@ -4,7 +4,7 @@ process MIRDEEP2_MAPPER {
     label 'process_medium'
     tag "$meta.id"
 
-    conda 'bioconda::mirdeep2=2.0.1.3'
+    conda 'bioconda::mirdeep2=2.0.1.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1' :
         'biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }"
@@ -14,8 +14,8 @@ process MIRDEEP2_MAPPER {
     path index
 
     output:
-    tuple path('*_collapsed.fa'), path('*reads_vs_refdb.arf'), emit: mirdeep2_inputs
-    path "versions.yml"                                      , emit: versions
+    tuple val(meta), path('*_collapsed.fa'), path('*reads_vs_refdb.arf'), emit: mirdeep2_inputs
+    path "versions.yml"                                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/mirdeep2_run.nf b/modules/local/mirdeep2_run.nf
@@ -4,20 +4,20 @@ process MIRDEEP2_RUN {
     label 'process_medium'
     errorStrategy 'ignore'
 
-    conda 'bioconda::mirdeep2=2.0.1.3'
+    conda 'bioconda::mirdeep2=2.0.1.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1' :
         'biocontainers/mirdeep2:2.0.1.3--hdfd78af_1' }"
 
     input:
     path(fasta)
-    tuple path(reads), path(arf)
+    tuple val(meta), path(reads), path(arf)
     path(hairpin)
     path(mature)
 
     output:
-    path 'result*.{bed,csv,html}', emit: result
-    path "versions.yml"          , emit: versions
+    tuple val(meta), path('result*.{bed,csv,html}'), emit: result
+    path "versions.yml"                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

diff --git a/modules/local/mirtop_quant.nf b/modules/local/mirtop_quant.nf
@@ -1,7 +1,7 @@
 process MIRTOP_QUANT {
     label 'process_medium'
 
-    conda 'mirtop=0.4.25 bioconda::samtools=1.15.1 conda-forge::r-base=4.1.1 conda-forge::r-data.table=1.14.2 python=3.7'
+    conda 'mirtop=0.4.25 bioconda::samtools=1.20 conda-forge::r-base=4.1.1 conda-forge::r-data.table=1.14.2 python=3.7'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' :
         'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }"

diff --git a/modules/local/parse_fasta_mirna.nf b/modules/local/parse_fasta_mirna.nf
@@ -1,7 +1,7 @@
 process PARSE_FASTA_MIRNA {
     label 'process_medium'
 
-    conda 'bioconda::seqkit=2.6.1'
+    conda 'bioconda::seqkit=2.8.2'
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqkit:2.6.1--h9ee0642_0' :
         'biocontainers/seqkit:2.6.1--h9ee0642_0' }"

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/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test
diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf