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Change path to tests
This commit is contained in:
drpatelh
parent
a87d584c48
commit
305d47fc87
23 changed files with 28 additions and 28 deletions
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@ -1,5 +1,5 @@
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- name: bowtie2 align single-end
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command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
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tags:
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- bowtie2
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- bowtie2_align_single_end
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@ -22,7 +22,7 @@
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should_exist: true
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- name: bowtie2 align paired-end
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command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
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tags:
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- bowtie2
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- bowtie2_align_paired_end
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@ -1,5 +1,5 @@
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- name: bowtie2 build
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command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config
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tags:
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- bowtie2
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- bowtie2_build
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@ -1,5 +1,5 @@
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- name: bwa index
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command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
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tags:
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- bwa
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- bwa_index
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@ -1,5 +1,5 @@
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- name: bwa mem single-end
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command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config
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tags:
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- bwa
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- bwa_mem
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@ -9,7 +9,7 @@
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md5sum: 3ee21210bac387e0335008146e4728bc
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- name: bwa mem paired-end
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command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
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tags:
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- bwa
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- bwa_mem
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@ -1,5 +1,5 @@
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- name: dsh filterbed
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command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config
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command: nextflow run ./tests/software/dsh/filterbed -entry test_dsh_filterbed -c tests/config/nextflow.config
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tags:
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- dsh
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- dsh_filterbed
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@ -1,5 +1,5 @@
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- name: dsh splitbed
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command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config
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command: nextflow run ./tests/software/dsh/splitbed -entry test_dsh_splitbed -c tests/config/nextflow.config
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tags:
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- dsh
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- dsh_splitbed
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- name: picard collectmultiplemetrics
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command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
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command: nextflow run ./tests/software/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
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tags:
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- picard
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- picard_collectmultiplemetrics
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- name: picard markduplicates on sorted bam
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command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
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command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
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tags:
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- picard
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- picard_markduplicates
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@ -9,7 +9,7 @@
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md5sum: 0ed0bfc94069380334ccd595f6d8207c
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- name: picard markduplicates on unsorted bam
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command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
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command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
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tags:
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- picard
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- picard_markduplicates
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- name: picard mergesamfiles
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command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config
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command: nextflow run ./tests/software/picard/mergesamfiles -entry test_picard_mergesamfiles -c tests/config/nextflow.config
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tags:
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- picard
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- picard_mergesamfiles
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@ -1,5 +1,5 @@
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- name: preseq lcextrap single-end
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command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_single_end -c tests/config/nextflow.config
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tags:
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- preseq
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- preseq_lcextrap
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@ -10,7 +10,7 @@
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- path: output/test_preseq_single_end/test.command.log
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- name: preseq lcextrap paired-end
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command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config
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tags:
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- preseq
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- preseq_lcextrap
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- name: salmon index
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command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config
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command: nextflow run ./tests/software/salmon/index -entry test_salmon_index -c tests/config/nextflow.config
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tags:
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- salmon
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- salmon_index
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- name: salmon quant single-end
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command: nextflow run ./tests/software/salmon -entry test_salmon_quant_single_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
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tags:
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- salmon
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- salmon_quant
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- name: samtools flagstat
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command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config
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command: nextflow run ./tests/software/samtools/flagstat -entry test_samtools_flagstat -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_flagstat
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- name: samtools idxstats
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command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config
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command: nextflow run ./tests/software/samtools/idxstats -entry test_samtools_idxstats -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_idxstats
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- name: samtools index
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command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config
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command: nextflow run ./tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_index
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- name: samtools mpileup
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command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config
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command: nextflow run ./tests/software/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_mpileup
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- name: samtools sort
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command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config
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command: nextflow run ./tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_sort
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- name: samtools stats
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command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config
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command: nextflow run ./tests/software/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_stats
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- name: samtools view
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command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config
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command: nextflow run ./tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools_view
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- name: seacr callpeak
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command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config
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command: nextflow run ./tests/software/seacr/callpeak -entry test_seacr_callpeak -c tests/config/nextflow.config
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tags:
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- seacr
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- seacr_callpeak
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- name: star align single-end
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command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/star/align -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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@ -37,7 +37,7 @@
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- name: star align paired-end
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command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config
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command: nextflow run ./tests/software/star/align -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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- name: star genomegenerate
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command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config
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command: nextflow run ./tests/software/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config
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tags:
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- star
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- star_genomegenerate
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- name: ucsc bedgraphtobigwig
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command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
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command: nextflow run ./tests/software/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
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tags:
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- ucsc_bedgraphtobigwig
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files:
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