From 688cc05fe86d1bef99ccf8e58946d0ccf846a6d9 Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Tue, 2 Feb 2021 15:30:59 -0600 Subject: [PATCH] tests: Remove -profile in tests See ddbca7b467b8f84b05d376bfcf7ff2c32e2588a5 for more info --- tests/software/bowtie/test.yml | 6 +++--- tests/software/bowtie2/test.yml | 6 +++--- tests/software/bwa/test.yml | 6 +++--- tests/software/cutadapt/test.yml | 4 ++-- tests/software/dsh/test.yml | 4 ++-- tests/software/fastp/test.yml | 4 ++-- tests/software/fastqc/test.yml | 4 ++-- tests/software/gffread/test.yml | 2 +- tests/software/multiqc/test.yml | 2 +- tests/software/pangolin/test.yml | 2 +- tests/software/picard/test.yml | 8 ++++---- tests/software/preseq/test.yml | 4 ++-- tests/software/quast/test.yml | 4 ++-- tests/software/salmon/test.yml | 6 +++--- tests/software/samtools/test.yml | 14 +++++++------- tests/software/seacr/test.yml | 2 +- tests/software/star/test.yml | 6 +++--- tests/software/stringtie/test.yml | 4 ++-- tests/software/trimgalore/test.yml | 4 ++-- tests/software/ucsc/test.yml | 2 +- 20 files changed, 47 insertions(+), 47 deletions(-) diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml index 96037548..61ed5f1d 100644 --- a/tests/software/bowtie/test.yml +++ b/tests/software/bowtie/test.yml @@ -1,5 +1,5 @@ - 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: - bowtie - bowtie_build @@ -18,7 +18,7 @@ md5sum: f3c398bba5158f4039334a932d79c051 - 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: - bowtie - bowtie_align @@ -41,7 +41,7 @@ md5sum: 9feed8a55d4b5e600dcc577768ef07fc - 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: - bowtie - bowtie_align diff --git a/tests/software/bowtie2/test.yml b/tests/software/bowtie2/test.yml index a3c6f31d..f5ecbf12 100644 --- a/tests/software/bowtie2/test.yml +++ b/tests/software/bowtie2/test.yml @@ -1,5 +1,5 @@ - 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: - bowtie2 - bowtie2_build @@ -18,7 +18,7 @@ md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72 - 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: - bowtie2 - bowtie2_align @@ -41,7 +41,7 @@ md5sum: 906102f401d8234b6473790988fb09cf - 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: - bowtie2 - bowtie2_align diff --git a/tests/software/bwa/test.yml b/tests/software/bwa/test.yml index 9efefa1d..3258af5a 100644 --- a/tests/software/bwa/test.yml +++ b/tests/software/bwa/test.yml @@ -1,5 +1,5 @@ - 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: - bwa - bwa_index @@ -14,7 +14,7 @@ md5sum: a47dcc92e750e2f16fbd979b8ff9538e - 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: - bwa - bwa_mem @@ -23,7 +23,7 @@ md5sum: 3ee21210bac387e0335008146e4728bc - 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: - bwa - bwa_mem diff --git a/tests/software/cutadapt/test.yml b/tests/software/cutadapt/test.yml index 39a06bc1..c91a0713 100644 --- a/tests/software/cutadapt/test.yml +++ b/tests/software/cutadapt/test.yml @@ -1,5 +1,5 @@ - 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: - cutadapt - cutadapt_se @@ -8,7 +8,7 @@ - path: ./output/cutadapt/test.trim.fastq.gz - 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: - cutadapt - cutadapt_pe diff --git a/tests/software/dsh/test.yml b/tests/software/dsh/test.yml index 3e4261b7..f58d2065 100644 --- a/tests/software/dsh/test.yml +++ b/tests/software/dsh/test.yml @@ -1,5 +1,5 @@ - 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: - dsh - dsh_filterbed @@ -8,7 +8,7 @@ md5sum: 91cee4392d6034793f99f6c53891d866 - 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: - dsh - dsh_splitbed diff --git a/tests/software/fastp/test.yml b/tests/software/fastp/test.yml index 56cbcaa7..5034c69a 100644 --- a/tests/software/fastp/test.yml +++ b/tests/software/fastp/test.yml @@ -1,5 +1,5 @@ - 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: - fastp - fastp_se @@ -12,7 +12,7 @@ - path: ./output/fastp/test.fastp.html - 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: - fastp - fastp_pe diff --git a/tests/software/fastqc/test.yml b/tests/software/fastqc/test.yml index f0f6b420..2c0862dd 100644 --- a/tests/software/fastqc/test.yml +++ b/tests/software/fastqc/test.yml @@ -1,5 +1,5 @@ - 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: - fastqc files: @@ -7,7 +7,7 @@ - path: output/test_single_end/test_fastqc.zip - 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: - fastqc files: diff --git a/tests/software/gffread/test.yml b/tests/software/gffread/test.yml index daf0cde8..a05e609d 100644 --- a/tests/software/gffread/test.yml +++ b/tests/software/gffread/test.yml @@ -1,5 +1,5 @@ - 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: - gffread files: diff --git a/tests/software/multiqc/test.yml b/tests/software/multiqc/test.yml index 7fc6d7a3..21dc36df 100644 --- a/tests/software/multiqc/test.yml +++ b/tests/software/multiqc/test.yml @@ -1,5 +1,5 @@ - 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: - multiqc files: diff --git a/tests/software/pangolin/test.yml b/tests/software/pangolin/test.yml index 2f44feb4..c50b4245 100644 --- a/tests/software/pangolin/test.yml +++ b/tests/software/pangolin/test.yml @@ -1,5 +1,5 @@ - 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: - pangolin files: diff --git a/tests/software/picard/test.yml b/tests/software/picard/test.yml index 91f62656..62554607 100644 --- a/tests/software/picard/test.yml +++ b/tests/software/picard/test.yml @@ -1,5 +1,5 @@ - 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: - picard - picard_mergesamfiles @@ -8,7 +8,7 @@ md5sum: a9c8a28d1aac362df5973ba2d9923f86 - 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: - picard - picard_collectmultiplemetrics @@ -25,7 +25,7 @@ - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics - 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: - picard - picard_markduplicates @@ -35,7 +35,7 @@ md5sum: 0ed0bfc94069380334ccd595f6d8207c - 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: - picard - picard_markduplicates diff --git a/tests/software/preseq/test.yml b/tests/software/preseq/test.yml index 14d940da..40eb6cdc 100644 --- a/tests/software/preseq/test.yml +++ b/tests/software/preseq/test.yml @@ -1,5 +1,5 @@ - 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: - preseq - preseq_lcextrap @@ -10,7 +10,7 @@ - path: output/test_preseq_single_end/test.command.log - 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: - preseq - preseq_lcextrap diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml index 2ceccc54..17a7f056 100644 --- a/tests/software/quast/test.yml +++ b/tests/software/quast/test.yml @@ -1,5 +1,5 @@ - 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: - quast - quast_reference @@ -88,7 +88,7 @@ - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf - 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: - quast - quast_no_reference diff --git a/tests/software/salmon/test.yml b/tests/software/salmon/test.yml index e5d09fe7..9febd8c1 100644 --- a/tests/software/salmon/test.yml +++ b/tests/software/salmon/test.yml @@ -1,5 +1,5 @@ - 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: - salmon - salmon_index @@ -31,7 +31,7 @@ md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 - 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: - salmon - salmon_quant @@ -85,7 +85,7 @@ md5sum: 27a76542337df436436e66017f66dd25 - 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: - salmon - salmon_quant diff --git a/tests/software/samtools/test.yml b/tests/software/samtools/test.yml index 5fc3b47c..c198cdd3 100644 --- a/tests/software/samtools/test.yml +++ b/tests/software/samtools/test.yml @@ -1,5 +1,5 @@ - 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: - samtools - samtools_flagstat @@ -8,7 +8,7 @@ md5sum: 80590621c74f5ee43ada20d010a3837f - 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: - samtools - samtools_idxstats @@ -17,7 +17,7 @@ md5sum: 3bee8b7d55e412da2b3816c5a18d60d5 - 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: - samtools - samtools_index @@ -26,7 +26,7 @@ md5sum: 67338c2995eae82c849830ca55aa7bd1 - 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: - samtools - samtools_sort @@ -35,7 +35,7 @@ md5sum: a41bfadacd2eeef1d31e05c135cc4f4e - 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: - samtools - samtools_stats @@ -44,7 +44,7 @@ md5sum: 06c183864d6e47ab89b0650cae831a93 - 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: - samtools - samtools_view @@ -53,7 +53,7 @@ md5sum: 7ea2c325e2249ed7ef44e1d9fdc4f8ff - 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: - samtools - samtools_mpileup diff --git a/tests/software/seacr/test.yml b/tests/software/seacr/test.yml index 88568d35..ed8306b1 100644 --- a/tests/software/seacr/test.yml +++ b/tests/software/seacr/test.yml @@ -1,5 +1,5 @@ - 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: - seacr - seacr_callpeak diff --git a/tests/software/star/test.yml b/tests/software/star/test.yml index fa7363fb..aca9595b 100644 --- a/tests/software/star/test.yml +++ b/tests/software/star/test.yml @@ -1,5 +1,5 @@ - 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: - star - star_genomegenerate @@ -32,7 +32,7 @@ md5sum: 8fbe69abbbef4f89da3854873984dbac - 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: - star - star_align @@ -70,7 +70,7 @@ md5sum: d41d8cd98f00b204e9800998ecf8427e - 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: - star - star_align diff --git a/tests/software/stringtie/test.yml b/tests/software/stringtie/test.yml index 21cea0e8..5bbf002b 100644 --- a/tests/software/stringtie/test.yml +++ b/tests/software/stringtie/test.yml @@ -1,5 +1,5 @@ - 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: - stringtie files: @@ -21,7 +21,7 @@ md5sum: 0106f70121a8b520d98b8739aed92915 - 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: - stringtie files: diff --git a/tests/software/trimgalore/test.yml b/tests/software/trimgalore/test.yml index 9ba4dddf..34d880db 100644 --- a/tests/software/trimgalore/test.yml +++ b/tests/software/trimgalore/test.yml @@ -1,5 +1,5 @@ - 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: - trimgalore files: @@ -9,7 +9,7 @@ - path: output/test_single_end/test_trimmed.fq.gz - 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: - trimgalore files: diff --git a/tests/software/ucsc/test.yml b/tests/software/ucsc/test.yml index 53be4e77..fae05063 100644 --- a/tests/software/ucsc/test.yml +++ b/tests/software/ucsc/test.yml @@ -1,5 +1,5 @@ - 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: - ucsc_bedgraphtobigwig files: