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https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
updated test md5sums
This commit is contained in:
kevinmenden
parent
71e0de733c
commit
a1e1e27f67
4 changed files with 133 additions and 24 deletions
40
.github/workflows/star_align.yml
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40
.github/workflows/star_align.yml
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name: star_genomegenerate
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on:
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push:
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paths:
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- software/star/align/**
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- .github/workflows/star_align.yml
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- tests/software/star/**
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pull_request:
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paths:
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- software/star/index/**
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- .github/workflows/star_align.yml
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- tests/software/star/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: pytest --tag star_genomegenerate --symlink --wt 2
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2
.github/workflows/star_genomegenerate.yml
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2
.github/workflows/star_genomegenerate.yml
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@ -7,7 +7,7 @@ on:
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- tests/software/star/**
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pull_request:
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paths:
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- software/star/index/**
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- software/star/genomegenerate/**
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- .github/workflows/star_genomegenerate.yml
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- tests/software/star/**
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@ -1,7 +1,7 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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def options_align = [args: '--readFilesCommand zcat --outSAMtype BAM Unsorted SortedByCoordinate']
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def options_align = [args: '--readFilesCommand zcat']
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def options_gg = [args: '--genomeSAindexNbases 9']
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include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: options_align )
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include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf' addParams( options: options_gg )
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@ -23,24 +23,14 @@ workflow test_star_alignment_single_end {
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STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf)
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}
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// workflow test_star_alignment_single_end {
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workflow test_star_alignment_paired_end {
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fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
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gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
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STAR_GENOMEGENERATE ( fasta, gtf )
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// fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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// BOWTIE_INDEX ( fasta )
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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// def input = []
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// input = [ [ id:'test', single_end:true ], // meta map
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// [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
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// BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
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// }
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// workflow test_star_alignment_paired_end {
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// fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
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// BOWTIE_INDEX ( fasta )
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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// file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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// BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
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// }
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STAR_ALIGN( input, STAR_GENOMEGENERATE.out.index, gtf)
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}
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@ -9,20 +9,19 @@
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- path: output/star/star/SA
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md5sum: 3e70e4fc6d031e1915bb510727f2c559
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- path: output/star/star/SAindex
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md5sum: 05a7baf30bda37f42f9fcf187a6e8247
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md5sum: a94198b95a245d4f64af2a7133b6ec7b
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- path: output/star/star/chrLength.txt
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md5sum: f2bea3725fe1c01420c57fb73bdeb31a
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- path: output/star/star/chrNameLength.txt
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md5sum: c7ceb0a8827b2ea91c386933bee48742
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- path: output/star/star/chrStart.txt
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md5sum: faf5c55020c99eceeef3e34188ac0d2f
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- path: output/star/star/exonGeTrInfo.tab
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md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
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- path: output/star/star/exonInfo.tab
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md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
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- path: output/star/star/genomeParameters.txt
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md5sum: ba83e83fc204d48534a1bb11f378076c
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md5sum: ed47b8b034cae2fefcdb39321aea47cd
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- path: output/star/star/sjdbInfo.txt
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md5sum: 1082ab459363b3f2f7aabcef0979c1ed
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- path: output/star/star/sjdbList.fromGTF.out.tab
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@ -31,3 +30,83 @@
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/star/star/transcriptInfo.tab
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md5sum: 8fbe69abbbef4f89da3854873984dbac
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- name: Run star single-end alignment
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command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_single_end -c tests/config/nextflow.config
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tags:
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- star
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- star_align
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- star_alignment_single_end
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files:
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- path: output/star/star/Genome
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md5sum: 323c992bac354f93073ce0fc43f222f8
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- path: output/star/star/SA
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md5sum: 3e70e4fc6d031e1915bb510727f2c559
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- path: output/star/star/SAindex
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md5sum: a94198b95a245d4f64af2a7133b6ec7b
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- path: output/star/star/chrLength.txt
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md5sum: f2bea3725fe1c01420c57fb73bdeb31a
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- path: output/star/star/chrNameLength.txt
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md5sum: c7ceb0a8827b2ea91c386933bee48742
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- path: output/star/star/chrStart.txt
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md5sum: faf5c55020c99eceeef3e34188ac0d2f
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- path: output/star/star/exonGeTrInfo.tab
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md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
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- path: output/star/star/exonInfo.tab
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md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
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- path: output/star/star/genomeParameters.txt
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md5sum: ed47b8b034cae2fefcdb39321aea47cd
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- path: output/star/star/sjdbInfo.txt
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md5sum: 1082ab459363b3f2f7aabcef0979c1ed
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- path: output/star/star/sjdbList.fromGTF.out.tab
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/star/star/sjdbList.out.tab
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/star/star/transcriptInfo.tab
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md5sum: 8fbe69abbbef4f89da3854873984dbac
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- path: output/star/test.Aligned.out.bam
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md5sum: d7f59c1728482e76a18e3f6eb9c66c25
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- path: output/star/test.Log.progress.out
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md5sum: b2bd061d6cbaaf3d6d3b1fed547f69b8
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- path: output/star/test.SJ.out.tab
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- name: Run star paired-end alignment
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command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_paired_end -c tests/config/nextflow.config
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tags:
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- star
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- star_align
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- star_alignment_paired_end
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files:
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- path: output/star/star/Genome
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md5sum: 323c992bac354f93073ce0fc43f222f8
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- path: output/star/star/SA
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md5sum: 3e70e4fc6d031e1915bb510727f2c559
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- path: output/star/star/SAindex
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md5sum: a94198b95a245d4f64af2a7133b6ec7b
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- path: output/star/star/chrLength.txt
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md5sum: f2bea3725fe1c01420c57fb73bdeb31a
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- path: output/star/star/chrNameLength.txt
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md5sum: c7ceb0a8827b2ea91c386933bee48742
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- path: output/star/star/chrStart.txt
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md5sum: faf5c55020c99eceeef3e34188ac0d2f
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- path: output/star/star/exonGeTrInfo.tab
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md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
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- path: output/star/star/exonInfo.tab
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md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
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- path: output/star/star/genomeParameters.txt
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md5sum: ed47b8b034cae2fefcdb39321aea47cd
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- path: output/star/star/sjdbInfo.txt
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md5sum: 1082ab459363b3f2f7aabcef0979c1ed
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- path: output/star/star/sjdbList.fromGTF.out.tab
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/star/star/sjdbList.out.tab
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/star/star/transcriptInfo.tab
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md5sum: 8fbe69abbbef4f89da3854873984dbac
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- path: output/star/test.Aligned.out.bam
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md5sum: 5c52bcaa15e86914ad6b895638235166
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- path: output/star/test.Log.progress.out
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md5sum: b2bd061d6cbaaf3d6d3b1fed547f69b8
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- path: output/star/test.SJ.out.tab
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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