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Fix lint
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@JoseEspinosa
JoseEspinosa committed Feb 5, 2024
1 parent 1b42a37 commit 334c21a
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Showing 3 changed files with 46 additions and 145 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/download_pipeline.yml
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Expand Up @@ -64,4 +64,4 @@ jobs:
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
4 changes: 2 additions & 2 deletions .nf-core.yml
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Expand Up @@ -3,5 +3,5 @@ repository_type: pipeline
lint:
nextflow_config:
- config_defaults:
- params.bamtools_filter_se_config
- params.bamtools_filter_pe_config
- params.bamtools_filter_se_config
- params.bamtools_filter_pe_config
185 changes: 43 additions & 142 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -8,259 +8,177 @@
"bowtie2/align": {
"branch": "master",
"git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
"installed_by": [
"fastq_align_bowtie2",
"modules"
]
"installed_by": ["fastq_align_bowtie2", "modules"]
},
"bowtie2/build": {
"branch": "master",
"git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"bwa/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"bwa/mem": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": [
"fastq_align_bwa",
"modules"
]
"installed_by": ["fastq_align_bwa", "modules"]
},
"chromap/chromap": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"fastq_align_chromap",
"modules"
]
"installed_by": ["fastq_align_chromap", "modules"]
},
"chromap/index": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"deeptools/computematrix": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"deeptools/plotfingerprint": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"deeptools/plotheatmap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"deeptools/plotprofile": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
"installed_by": [
"fastq_fastqc_umitools_trimgalore",
"modules"
]
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
},
"gffread": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"homer/annotatepeaks": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"khmer/uniquekmers": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"macs2/callpeak": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"phantompeakqualtools": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
"installed_by": [
"bam_markduplicates_picard",
"modules"
]
"installed_by": ["bam_markduplicates_picard", "modules"]
},
"picard/mergesamfiles": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"preseq/lcextrap": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": [
"bam_stats_samtools",
"modules"
]
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": [
"bam_stats_samtools",
"modules"
]
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": [
"bam_markduplicates_picard",
"bam_sort_stats_samtools",
"modules"
]
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools", "modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
"installed_by": [
"bam_sort_stats_samtools",
"modules"
]
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "ec833ac4c29db6005d18baccf3306f557c46b006",
"installed_by": [
"bam_stats_samtools",
"modules"
]
"installed_by": ["bam_stats_samtools", "modules"]
},
"subread/featurecounts": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"trimgalore": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": [
"fastq_fastqc_umitools_trimgalore",
"modules"
]
"installed_by": ["fastq_fastqc_umitools_trimgalore", "modules"]
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"installed_by": [
"fastq_fastqc_umitools_trimgalore"
]
"installed_by": ["fastq_fastqc_umitools_trimgalore"]
},
"untar": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
},
"untarfiles": {
"branch": "master",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": [
"modules"
]
"installed_by": ["modules"]
}
}
},
Expand All @@ -269,57 +187,40 @@
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"installed_by": [
"fastq_align_bowtie2",
"fastq_align_bwa",
"fastq_align_chromap"
]
"installed_by": ["fastq_align_bowtie2", "fastq_align_bwa", "fastq_align_chromap"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"installed_by": [
"bam_markduplicates_picard",
"bam_sort_stats_samtools"
]
"installed_by": ["bam_markduplicates_picard", "bam_sort_stats_samtools"]
},
"fastq_align_bowtie2": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"fastq_align_bwa": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"fastq_align_chromap": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": [
"subworkflows"
]
"installed_by": ["subworkflows"]
}
}
}
}
}
}
}

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