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Fixed linting #377

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Aug 19, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -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".

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30 changes: 15 additions & 15 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand All @@ -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": {
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2 changes: 1 addition & 1 deletion modules/local/bowtie_map_mirna.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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' }"
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2 changes: 1 addition & 1 deletion modules/local/edger_qc.nf
Original file line number Diff line number Diff line change
@@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0' :
'biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0' }"
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6 changes: 3 additions & 3 deletions modules/local/mirdeep2_mapper.nf
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ process MIRDEEP2_MAPPER {
label 'process_medium'
tag "$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' }"
Expand All @@ -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
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8 changes: 4 additions & 4 deletions modules/local/mirdeep2_run.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/local/mirtop_quant.nf
Original file line number Diff line number Diff line change
@@ -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' }"
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2 changes: 1 addition & 1 deletion modules/local/parse_fasta_mirna.nf
Original file line number Diff line number Diff line change
@@ -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' }"
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1 change: 0 additions & 1 deletion modules/nf-core/cat/cat/main.nf

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27 changes: 20 additions & 7 deletions modules/nf-core/cat/cat/tests/main.nf.test

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74 changes: 50 additions & 24 deletions modules/nf-core/cat/cat/tests/main.nf.test.snap

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10 changes: 5 additions & 5 deletions modules/nf-core/cat/fastq/main.nf

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