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yevis-metadata_nf-core_rnaseq_small_test.yml
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yevis-metadata_nf-core_rnaseq_small_test.yml
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---
id: 20da6ea5-de91-4973-ac20-216882357a0d
version: 1.0.0
license: CC0-1.0
authors:
- github_account: suecharo
name: Hirotaka Suetake
affiliation: "The University of Tokyo"
orcid: 0000-0003-2765-0049
workflow:
name: nf-core - rnaseq - v3.7 with Small Test Data
readme: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/README.md"
language:
type: NFL
version: "1.0"
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target: README.md
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type: secondary
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target: assets/schema_input.json
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target: bin/check_samplesheet.py
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target: bin/filter_gtf_for_genes_in_genome.py
type: secondary
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target: bin/salmon_summarizedexperiment.r
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target: bin/salmon_tx2gene.py
type: secondary
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target: bin/salmon_tximport.r
type: secondary
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target: conf/base.config
type: secondary
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target: conf/igenomes.config
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type: secondary
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target: modules/local/gtf2bed.nf
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target: modules/local/multiqc_tsv_from_list.nf
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target: modules/nf-core/modules/preseq/lcextrap/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/preseq/lcextrap/meta.yml"
target: modules/nf-core/modules/preseq/lcextrap/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/qualimap/rnaseq/main.nf"
target: modules/nf-core/modules/qualimap/rnaseq/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rsem/calculateexpression/main.nf"
target: modules/nf-core/modules/rsem/calculateexpression/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rsem/calculateexpression/meta.yml"
target: modules/nf-core/modules/rsem/calculateexpression/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rsem/preparereference/main.nf"
target: modules/nf-core/modules/rsem/preparereference/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rsem/preparereference/meta.yml"
target: modules/nf-core/modules/rsem/preparereference/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/bamstat/main.nf"
target: modules/nf-core/modules/rseqc/bamstat/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/bamstat/meta.yml"
target: modules/nf-core/modules/rseqc/bamstat/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/inferexperiment/main.nf"
target: modules/nf-core/modules/rseqc/inferexperiment/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/inferexperiment/meta.yml"
target: modules/nf-core/modules/rseqc/inferexperiment/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/innerdistance/main.nf"
target: modules/nf-core/modules/rseqc/innerdistance/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/innerdistance/meta.yml"
target: modules/nf-core/modules/rseqc/innerdistance/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/junctionannotation/main.nf"
target: modules/nf-core/modules/rseqc/junctionannotation/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/junctionannotation/meta.yml"
target: modules/nf-core/modules/rseqc/junctionannotation/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/junctionsaturation/main.nf"
target: modules/nf-core/modules/rseqc/junctionsaturation/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/junctionsaturation/meta.yml"
target: modules/nf-core/modules/rseqc/junctionsaturation/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/readdistribution/main.nf"
target: modules/nf-core/modules/rseqc/readdistribution/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/readdistribution/meta.yml"
target: modules/nf-core/modules/rseqc/readdistribution/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/readduplication/main.nf"
target: modules/nf-core/modules/rseqc/readduplication/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/readduplication/meta.yml"
target: modules/nf-core/modules/rseqc/readduplication/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/tin/main.nf"
target: modules/nf-core/modules/rseqc/tin/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/rseqc/tin/meta.yml"
target: modules/nf-core/modules/rseqc/tin/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/salmon/index/main.nf"
target: modules/nf-core/modules/salmon/index/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/salmon/index/meta.yml"
target: modules/nf-core/modules/salmon/index/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/salmon/quant/main.nf"
target: modules/nf-core/modules/salmon/quant/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/salmon/quant/meta.yml"
target: modules/nf-core/modules/salmon/quant/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/flagstat/main.nf"
target: modules/nf-core/modules/samtools/flagstat/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/flagstat/meta.yml"
target: modules/nf-core/modules/samtools/flagstat/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/idxstats/main.nf"
target: modules/nf-core/modules/samtools/idxstats/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/idxstats/meta.yml"
target: modules/nf-core/modules/samtools/idxstats/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/index/main.nf"
target: modules/nf-core/modules/samtools/index/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/index/meta.yml"
target: modules/nf-core/modules/samtools/index/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/sort/main.nf"
target: modules/nf-core/modules/samtools/sort/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/sort/meta.yml"
target: modules/nf-core/modules/samtools/sort/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/stats/main.nf"
target: modules/nf-core/modules/samtools/stats/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/samtools/stats/meta.yml"
target: modules/nf-core/modules/samtools/stats/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/sortmerna/main.nf"
target: modules/nf-core/modules/sortmerna/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/stringtie/stringtie/main.nf"
target: modules/nf-core/modules/stringtie/stringtie/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/stringtie/stringtie/meta.yml"
target: modules/nf-core/modules/stringtie/stringtie/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/subread/featurecounts/main.nf"
target: modules/nf-core/modules/subread/featurecounts/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/subread/featurecounts/meta.yml"
target: modules/nf-core/modules/subread/featurecounts/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/trimgalore/main.nf"
target: modules/nf-core/modules/trimgalore/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/trimgalore/meta.yml"
target: modules/nf-core/modules/trimgalore/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/ucsc/bedclip/main.nf"
target: modules/nf-core/modules/ucsc/bedclip/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/ucsc/bedclip/meta.yml"
target: modules/nf-core/modules/ucsc/bedclip/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf"
target: modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/ucsc/bedgraphtobigwig/meta.yml"
target: modules/nf-core/modules/ucsc/bedgraphtobigwig/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/umitools/dedup/main.nf"
target: modules/nf-core/modules/umitools/dedup/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/umitools/dedup/meta.yml"
target: modules/nf-core/modules/umitools/dedup/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/umitools/extract/main.nf"
target: modules/nf-core/modules/umitools/extract/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/umitools/extract/meta.yml"
target: modules/nf-core/modules/umitools/extract/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/untar/main.nf"
target: modules/nf-core/modules/untar/main.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/modules/nf-core/modules/untar/meta.yml"
target: modules/nf-core/modules/untar/meta.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/nextflow.config"
target: nextflow.config
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/nextflow_schema.json"
target: nextflow_schema.json
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/local/align_star.nf"
target: subworkflows/local/align_star.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/local/input_check.nf"
target: subworkflows/local/input_check.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/local/prepare_genome.nf"
target: subworkflows/local/prepare_genome.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/local/quantify_rsem.nf"
target: subworkflows/local/quantify_rsem.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/local/quantify_salmon.nf"
target: subworkflows/local/quantify_salmon.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/align_hisat2.nf"
target: subworkflows/nf-core/align_hisat2.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/bam_sort_samtools.nf"
target: subworkflows/nf-core/bam_sort_samtools.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/bam_stats_samtools.nf"
target: subworkflows/nf-core/bam_stats_samtools.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/bedgraph_to_bigwig.nf"
target: subworkflows/nf-core/bedgraph_to_bigwig.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/dedup_umi_umitools.nf"
target: subworkflows/nf-core/dedup_umi_umitools.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/fastqc_umitools_trimgalore.nf"
target: subworkflows/nf-core/fastqc_umitools_trimgalore.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/mark_duplicates_picard.nf"
target: subworkflows/nf-core/mark_duplicates_picard.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/subworkflows/nf-core/rseqc.nf"
target: subworkflows/nf-core/rseqc.nf
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/tower.yml"
target: tower.yml
type: secondary
- url: "https://raw.githubusercontent.com/nf-core/rnaseq/e0dfce9af5c2299bcc2b8a74b6559ce055965455/workflows/rnaseq.nf"
target: workflows/rnaseq.nf
type: secondary
testing:
- id: example_test
files:
- url: "https://github.com/sapporo-wes/test-workflow/blob/main/assets/nf-core_rnaseq_wf_params.json"
target: wf_params.json
type: wf_params
- url: "https://gist.github.com/e42b4a98990ac8894a975223d41bfaeb"
target: wf_engine_params.json
type: wf_engine_params
- url: "https://github.com/sapporo-wes/test-workflow/blob/main/assets/nf-core_rnaseq_samplesheet_small_test.csv"
target: nf-core_rnaseq_samplesheet_small_test.csv
type: other