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tests: Remove -profile in tests

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See ddbca7b467 for more info
This commit is contained in:
Edmund Miller 2021-02-02 15:30:59 -06:00
parent 35ac5c5f15
commit 688cc05fe8
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GPG key ID: BD387FF7BC10AA9D
20 changed files with 47 additions and 47 deletions
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6
tests/software/bowtie/test.yml
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@ -1,5 +1,5 @@
- name: Run bowtie build - name: Run bowtie build
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_build -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie -entry test_bowtie_build -c tests/config/nextflow.config
tags: tags:
- bowtie - bowtie
- bowtie_build - bowtie_build
@ -18,7 +18,7 @@
md5sum: f3c398bba5158f4039334a932d79c051 md5sum: f3c398bba5158f4039334a932d79c051
- name: Run bowtie build and align single-end - name: Run bowtie build and align single-end
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
tags: tags:
- bowtie - bowtie
- bowtie_align - bowtie_align
@ -41,7 +41,7 @@
md5sum: 9feed8a55d4b5e600dcc577768ef07fc md5sum: 9feed8a55d4b5e600dcc577768ef07fc
- name: Run bowtie index and align paired-end - name: Run bowtie index and align paired-end
command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie -entry test_bowtie_alignment_paired_end -c tests/config/nextflow.config
tags: tags:
- bowtie - bowtie
- bowtie_align - bowtie_align

6
tests/software/bowtie2/test.yml
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@ -1,5 +1,5 @@
- name: Run bowtie2 build - name: Run bowtie2 build
command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_build -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config
tags: tags:
- bowtie2 - bowtie2
- bowtie2_build - bowtie2_build
@ -18,7 +18,7 @@
md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- name: Run bowtie2 index and align single-end - name: Run bowtie2 index and align single-end
command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_single_end -c tests/config/nextflow.config
tags: tags:
- bowtie2 - bowtie2
- bowtie2_align - bowtie2_align
@ -41,7 +41,7 @@
md5sum: 906102f401d8234b6473790988fb09cf md5sum: 906102f401d8234b6473790988fb09cf
- name: Run bowtie2 index and align paired-end - name: Run bowtie2 index and align paired-end
command: nextflow run ./tests/software/bowtie2 -profile docker -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_alignment_paired_end -c tests/config/nextflow.config
tags: tags:
- bowtie2 - bowtie2
- bowtie2_align - bowtie2_align

6
tests/software/bwa/test.yml
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@ -1,5 +1,5 @@
- name: Run bwa index - name: Run bwa index
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config
tags: tags:
- bwa - bwa
- bwa_index - bwa_index
@ -14,7 +14,7 @@
md5sum: a47dcc92e750e2f16fbd979b8ff9538e md5sum: a47dcc92e750e2f16fbd979b8ff9538e
- name: Run bwa mem single-end - name: Run bwa mem single-end
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config
tags: tags:
- bwa - bwa
- bwa_mem - bwa_mem
@ -23,7 +23,7 @@
md5sum: 3ee21210bac387e0335008146e4728bc md5sum: 3ee21210bac387e0335008146e4728bc
- name: Run bwa mem paired-end - name: Run bwa mem paired-end
command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
tags: tags:
- bwa - bwa
- bwa_mem - bwa_mem

4
tests/software/cutadapt/test.yml
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@ -1,5 +1,5 @@
- name: Run cutadapt single-end test workflow - name: Run cutadapt single-end test workflow
command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_se -c tests/config/nextflow.config command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_se -c tests/config/nextflow.config
tags: tags:
- cutadapt - cutadapt
- cutadapt_se - cutadapt_se
@ -8,7 +8,7 @@
- path: ./output/cutadapt/test.trim.fastq.gz - path: ./output/cutadapt/test.trim.fastq.gz
- name: Run cutadapt paired-end test workflow - name: Run cutadapt paired-end test workflow
command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_pe -c tests/config/nextflow.config command: nextflow run ./tests/software/cutadapt -entry test_cutadapt_pe -c tests/config/nextflow.config
tags: tags:
- cutadapt - cutadapt
- cutadapt_pe - cutadapt_pe

4
tests/software/dsh/test.yml
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@ -1,5 +1,5 @@
- name: Run dsh filterbed - name: Run dsh filterbed
command: nextflow run ./tests/software/dsh -profile docker -entry test_dsh_filterbed -c tests/config/nextflow.config command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config
tags: tags:
- dsh - dsh
- dsh_filterbed - dsh_filterbed
@ -8,7 +8,7 @@
md5sum: 91cee4392d6034793f99f6c53891d866 md5sum: 91cee4392d6034793f99f6c53891d866
- name: Run dsh splitbed - name: Run dsh splitbed
command: nextflow run ./tests/software/dsh -profile docker -entry test_dsh_splitbed -c tests/config/nextflow.config command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config
tags: tags:
- dsh - dsh
- dsh_splitbed - dsh_splitbed

4
tests/software/fastp/test.yml
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@ -1,5 +1,5 @@
- name: fastp_se - name: fastp_se
command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_se -c ./tests/config/nextflow.config command: nextflow run ./tests/software/fastp -entry test_fastp_se -c ./tests/config/nextflow.config
tags: tags:
- fastp - fastp
- fastp_se - fastp_se
@ -12,7 +12,7 @@
- path: ./output/fastp/test.fastp.html - path: ./output/fastp/test.fastp.html
- name: fastp_pe - name: fastp_pe
command: nextflow run ./tests/software/fastp -profile docker -entry test_fastp_pe -c ./tests/config/nextflow.config command: nextflow run ./tests/software/fastp -entry test_fastp_pe -c ./tests/config/nextflow.config
tags: tags:
- fastp - fastp
- fastp_pe - fastp_pe

4
tests/software/fastqc/test.yml
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@ -1,5 +1,5 @@
- name: Run fastqc single-end test workflow - name: Run fastqc single-end test workflow
command: nextflow run ./tests/software/fastqc/ -profile docker -entry test_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/fastqc/ -entry test_single_end -c tests/config/nextflow.config
tags: tags:
- fastqc - fastqc
files: files:
@ -7,7 +7,7 @@
- path: output/test_single_end/test_fastqc.zip - path: output/test_single_end/test_fastqc.zip
- name: Run fastqc paired-end test workflow - name: Run fastqc paired-end test workflow
command: nextflow run ./tests/software/fastqc/ -profile docker -entry test_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/fastqc/ -entry test_paired_end -c tests/config/nextflow.config
tags: tags:
- fastqc - fastqc
files: files:

2
tests/software/gffread/test.yml
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@ -1,5 +1,5 @@
- name: Run gffread test workflow - name: Run gffread test workflow
command: nextflow run ./tests/software/gffread/ -profile docker -entry test_gffread -c tests/config/nextflow.config command: nextflow run ./tests/software/gffread/ -entry test_gffread -c tests/config/nextflow.config
tags: tags:
- gffread - gffread
files: files:

2
tests/software/multiqc/test.yml
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@ -1,5 +1,5 @@
- name: Run multiqc test workflow - name: Run multiqc test workflow
command: nextflow run ./tests/software/multiqc/ -profile docker -entry test_multiqc -c tests/config/nextflow.config command: nextflow run ./tests/software/multiqc/ -entry test_multiqc -c tests/config/nextflow.config
tags: tags:
- multiqc - multiqc
files: files:

2
tests/software/pangolin/test.yml
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@ -1,5 +1,5 @@
- name: pangolin - name: pangolin
command: nextflow run ./tests/software/pangolin -profile docker -entry test_pangolin -c ./tests/config/nextflow.config command: nextflow run ./tests/software/pangolin -entry test_pangolin -c ./tests/config/nextflow.config
tags: tags:
- pangolin - pangolin
files: files:

8
tests/software/picard/test.yml
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@ -1,5 +1,5 @@
- name: Run picard mergesamfiles - name: Run picard mergesamfiles
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config
tags: tags:
- picard - picard
- picard_mergesamfiles - picard_mergesamfiles
@ -8,7 +8,7 @@
md5sum: a9c8a28d1aac362df5973ba2d9923f86 md5sum: a9c8a28d1aac362df5973ba2d9923f86
- name: Run picard collectmultiplemetrics - name: Run picard collectmultiplemetrics
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
tags: tags:
- picard - picard
- picard_collectmultiplemetrics - picard_collectmultiplemetrics
@ -25,7 +25,7 @@
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
- name: Run picard MarkDuplicates - name: Run picard MarkDuplicates
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates -c tests/config/nextflow.config command: nextflow run ./tests/software/picard -entry test_picard_markduplicates -c tests/config/nextflow.config
tags: tags:
- picard - picard
- picard_markduplicates - picard_markduplicates
@ -35,7 +35,7 @@
md5sum: 0ed0bfc94069380334ccd595f6d8207c md5sum: 0ed0bfc94069380334ccd595f6d8207c
- name: Run picard MarkDuplicates without a sorted bam file so it fails - name: Run picard MarkDuplicates without a sorted bam file so it fails
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
tags: tags:
- picard - picard
- picard_markduplicates - picard_markduplicates

4
tests/software/preseq/test.yml
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@ -1,5 +1,5 @@
- name: Run preseq single-end lcextrap - name: Run preseq single-end lcextrap
command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config
tags: tags:
- preseq - preseq
- preseq_lcextrap - preseq_lcextrap
@ -10,7 +10,7 @@
- path: output/test_preseq_single_end/test.command.log - path: output/test_preseq_single_end/test.command.log
- name: Run preseq paired-end lcextrap - name: Run preseq paired-end lcextrap
command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config
tags: tags:
- preseq - preseq
- preseq_lcextrap - preseq_lcextrap

4
tests/software/quast/test.yml
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@ -1,5 +1,5 @@
- name: quast_ref - name: quast_ref
command: nextflow run ./tests/software/quast -profile docker -entry test_quast_ref -c ./tests/config/nextflow.config command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
tags: tags:
- quast - quast
- quast_reference - quast_reference
@ -88,7 +88,7 @@
- path: ./output/quast/quast/aligned_stats/NAx_plot.pdf - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
- name: quast_noref - name: quast_noref
command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
tags: tags:
- quast - quast
- quast_no_reference - quast_no_reference

6
tests/software/salmon/test.yml
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@ -1,5 +1,5 @@
- name: salmon index - name: salmon index
command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_index -c tests/config/nextflow.config command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config
tags: tags:
- salmon - salmon
- salmon_index - salmon_index
@ -31,7 +31,7 @@
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- name: salmon quant paired end - name: salmon quant paired end
command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_pe -c tests/config/nextflow.config command: nextflow run ./tests/software/salmon -entry test_salmon_quant_pe -c tests/config/nextflow.config
tags: tags:
- salmon - salmon
- salmon_quant - salmon_quant
@ -85,7 +85,7 @@
md5sum: 27a76542337df436436e66017f66dd25 md5sum: 27a76542337df436436e66017f66dd25
- name: salmon quant single-end - name: salmon quant single-end
command: nextflow run ./tests/software/salmon -profile docker -entry test_salmon_quant_se -c tests/config/nextflow.config command: nextflow run ./tests/software/salmon -entry test_salmon_quant_se -c tests/config/nextflow.config
tags: tags:
- salmon - salmon
- salmon_quant - salmon_quant

14
tests/software/samtools/test.yml
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@ -1,5 +1,5 @@
- name: Run samtools flagstat test workflow - name: Run samtools flagstat test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_flagstat -c tests/config/nextflow.config command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_flagstat - samtools_flagstat
@ -8,7 +8,7 @@
md5sum: 80590621c74f5ee43ada20d010a3837f md5sum: 80590621c74f5ee43ada20d010a3837f
- name: Run samtools idxstats test workflow - name: Run samtools idxstats test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_idxstats - samtools_idxstats
@ -17,7 +17,7 @@
md5sum: 3bee8b7d55e412da2b3816c5a18d60d5 md5sum: 3bee8b7d55e412da2b3816c5a18d60d5
- name: Run samtools index test workflow - name: Run samtools index test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_index -c tests/config/nextflow.config command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_index - samtools_index
@ -26,7 +26,7 @@
md5sum: 67338c2995eae82c849830ca55aa7bd1 md5sum: 67338c2995eae82c849830ca55aa7bd1
- name: Run samtools sort test workflow - name: Run samtools sort test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_sort -c tests/config/nextflow.config command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_sort - samtools_sort
@ -35,7 +35,7 @@
md5sum: a41bfadacd2eeef1d31e05c135cc4f4e md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
- name: Run samtools stats test workflow - name: Run samtools stats test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_stats -c tests/config/nextflow.config command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_stats - samtools_stats
@ -44,7 +44,7 @@
md5sum: 06c183864d6e47ab89b0650cae831a93 md5sum: 06c183864d6e47ab89b0650cae831a93
- name: Run samtools view test workflow - name: Run samtools view test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_view -c tests/config/nextflow.config command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_view - samtools_view
@ -53,7 +53,7 @@
md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff
- name: Run samtools mpileup test workflow - name: Run samtools mpileup test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_mpileup -c tests/config/nextflow.config command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config
tags: tags:
- samtools - samtools
- samtools_mpileup - samtools_mpileup

2
tests/software/seacr/test.yml
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@ -1,5 +1,5 @@
- name: Run seacr call peak test workflow - name: Run seacr call peak test workflow
command: nextflow run ./tests/software/seacr/ -profile docker -entry test_seacr_callpeak -c tests/config/nextflow.config command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config
tags: tags:
- seacr - seacr
- seacr_callpeak - seacr_callpeak

6
tests/software/star/test.yml
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@ -1,5 +1,5 @@
- name: Run star genomegenerate - name: Run star genomegenerate
command: nextflow run ./tests/software/star -profile docker -entry test_star_genomegenerate -c tests/config/nextflow.config command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config
tags: tags:
- star - star
- star_genomegenerate - star_genomegenerate
@ -32,7 +32,7 @@
md5sum: 8fbe69abbbef4f89da3854873984dbac md5sum: 8fbe69abbbef4f89da3854873984dbac
- name: Run star single-end alignment - name: Run star single-end alignment
command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config
tags: tags:
- star - star
- star_align - star_align
@ -70,7 +70,7 @@
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- name: Run star paired-end alignment - name: Run star paired-end alignment
command: nextflow run ./tests/software/star -profile docker -entry test_star_alignment_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config
tags: tags:
- star - star
- star_align - star_align

4
tests/software/stringtie/test.yml
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@ -1,5 +1,5 @@
- name: Run stringtie forward strand test workflow - name: Run stringtie forward strand test workflow
command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_forward -c tests/config/nextflow.config command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_forward -c tests/config/nextflow.config
tags: tags:
- stringtie - stringtie
files: files:
@ -21,7 +21,7 @@
md5sum: 0106f70121a8b520d98b8739aed92915 md5sum: 0106f70121a8b520d98b8739aed92915
- name: Run stringtie reverse strand test workflow - name: Run stringtie reverse strand test workflow
command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_reverse -c tests/config/nextflow.config command: nextflow run ./tests/software/stringtie/ -entry test_stringtie_reverse -c tests/config/nextflow.config
tags: tags:
- stringtie - stringtie
files: files:

4
tests/software/trimgalore/test.yml
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@ -1,5 +1,5 @@
- name: Run trimgalore single-end test workflow - name: Run trimgalore single-end test workflow
command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_single_end -c tests/config/nextflow.config
tags: tags:
- trimgalore - trimgalore
files: files:
@ -9,7 +9,7 @@
- path: output/test_single_end/test_trimmed.fq.gz - path: output/test_single_end/test_trimmed.fq.gz
- name: Run trimgalore paired-end test workflow - name: Run trimgalore paired-end test workflow
command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/trimgalore/ -entry test_trimgalore_paired_end -c tests/config/nextflow.config
tags: tags:
- trimgalore - trimgalore
files: files:

2
tests/software/ucsc/test.yml
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@ -1,5 +1,5 @@
- name: Run bedgraphtobigwig test workflow - name: Run bedgraphtobigwig test workflow
command: nextflow run ./tests/software/ucsc/ -profile docker -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
tags: tags:
- ucsc_bedgraphtobigwig - ucsc_bedgraphtobigwig
files: files: