From 3e0b3e96de08e740646d20bdf08c79ebde4b2c60 Mon Sep 17 00:00:00 2001 From: egreenberg7 Date: Thu, 19 Sep 2024 11:52:30 -0400 Subject: [PATCH] (Hopefully) final linting fix --- modules.json | 286 ++++++++++++--------------------------------------- 1 file changed, 68 insertions(+), 218 deletions(-) diff --git a/modules.json b/modules.json index 82e0e34be..4c9ba76f1 100644 --- a/modules.json +++ b/modules.json @@ -8,272 +8,189 @@ "bbmap/bbsplit": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "modules" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "bedtools/genomecov": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bracken/bracken": { "branch": "master", "git_sha": "c214fad97b328eb6d6233f779be9ba44814a9136", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "modules" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "custom/catadditionalfasta": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/tx2gene": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "dupradar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastp": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_fastp", - "modules" - ] + "installed_by": ["fastq_fastqc_umitools_fastp", "modules"] }, "fastqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_fastp", - "fastq_fastqc_umitools_trimgalore" - ] + "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "fq/subsample": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_subsample_fq_salmon", - "modules" - ] + "installed_by": ["fastq_subsample_fq_salmon", "modules"] }, "gffread": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/align": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": [ - "fastq_align_hisat2" - ], + "installed_by": ["fastq_align_hisat2"], "patch": "modules/nf-core/hisat2/align/hisat2-align.diff" }, "hisat2/build": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hisat2/extractsplicesites": { "branch": "master", "git_sha": "ad30f90cfc383dfaa505771d24f9e292c53157ab", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kallisto/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "kallisto/quant": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "kraken2/kraken2": { "branch": "master", "git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "picard/markduplicates": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_markduplicates_picard" - ], + "installed_by": ["bam_markduplicates_picard"], "patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff" }, "preseq/lcextrap": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "qualimap/rnaseq": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rsem/calculateexpression": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rsem/preparereference": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rseqc/bamstat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/inferexperiment": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/innerdistance": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/junctionannotation": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/junctionsaturation": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/readdistribution": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/readduplication": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "rseqc/tin": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_rseqc" - ] + "installed_by": ["bam_rseqc"] }, "salmon/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_subsample_fq_salmon" - ] + "installed_by": ["fastq_subsample_fq_salmon"] }, "salmon/quant": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_subsample_fq_salmon", - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["fastq_subsample_fq_salmon", "modules", "quantify_pseudo_alignment"] }, "samtools/flagstat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", @@ -287,118 +204,82 @@ "samtools/sort": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "sortmerna": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "modules" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"] }, "star/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "star/genomegenerate": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "stringtie/stringtie": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "summarizedexperiment/summarizedexperiment": { "branch": "master", "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "trimgalore": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_trimgalore" - ] + "installed_by": ["fastq_fastqc_umitools_trimgalore"] }, "tximeta/tximport": { "branch": "master", "git_sha": "625fbbc0531fb1717349c7f1b1c677a3b8619767", - "installed_by": [ - "modules", - "quantify_pseudo_alignment" - ] + "installed_by": ["modules", "quantify_pseudo_alignment"] }, "ucsc/bedclip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bedgraph_bedclip_bedgraphtobigwig" - ] + "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "ucsc/bedgraphtobigwig": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bedgraph_bedclip_bedgraphtobigwig" - ] + "installed_by": ["bedgraph_bedclip_bedgraphtobigwig"] }, "umitools/dedup": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "bam_dedup_stats_samtools_umitools" - ] + "installed_by": ["bam_dedup_stats_samtools_umitools"] }, "umitools/extract": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "fastq_fastqc_umitools_fastp", - "fastq_fastqc_umitools_trimgalore" - ] + "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"] }, "umitools/prepareforrsem": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -407,30 +288,22 @@ "bam_dedup_stats_samtools_umitools": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_markduplicates_picard": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_rseqc": { "branch": "master", "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_sort_stats_samtools": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "fastq_align_hisat2" - ] + "installed_by": ["fastq_align_hisat2"] }, "bam_stats_samtools": { "branch": "master", @@ -444,78 +317,55 @@ "bedgraph_bedclip_bedgraphtobigwig": { "branch": "master", "git_sha": "0eacd714effe5aac1c1de26593873960b3346cab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_align_hisat2": { "branch": "master", "git_sha": "c789476080a150f87066ca3ed42a622339a26c0b", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_fastqc_umitools_fastp": { "branch": "master", "git_sha": "46eca555142d6e597729fcb682adcc791796f514", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "subworkflows" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_fastqc_umitools_trimgalore": { "branch": "master", "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "subworkflows" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "fastq_qc_trim_filter_setstrandedness": { "branch": "master", "git_sha": "ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "fastq_subsample_fq_salmon": { "branch": "master", "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", - "installed_by": [ - "fastq_qc_trim_filter_setstrandedness", - "subworkflows" - ] + "installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"] }, "quantify_pseudo_alignment": { "branch": "master", "git_sha": "fbe341e9af0bb98533757f536b26d38507d31724", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +}