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Add default output dir for modules that create indices, updated (#336)

Browse source 
* Add default output dir for modules that create indices

* Change path for index module test output

* Fix bowtie2/align tests

* Fixing bowtie/align tests

* Fix genomegenerate test

* Fixing README linting
This commit is contained in:
Jose Espinosa-Carrasco 2021-03-23 18:55:01 +01:00 committed by GitHub
parent d6850f8312
commit ee90e7af77
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
19 changed files with 93 additions and 94 deletions
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2
software/bowtie/build/main.nf
View file

@ -9,7 +9,7 @@ process BOWTIE_BUILD {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/bowtie2/build/main.nf
View file

@ -9,7 +9,7 @@ process BOWTIE2_BUILD {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null) conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/bwa/index/main.nf
View file

@ -9,7 +9,7 @@ process BWA_INDEX {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/bwamem2/index/main.nf
View file

@ -9,7 +9,7 @@ process BWAMEM2_INDEX {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? "bioconda::bwa-mem2=2.1" : null) conda (params.enable_conda ? "bioconda::bwa-mem2=2.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/bwameth/index/main.nf
View file

@ -9,7 +9,7 @@ process BWAMETH_INDEX {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/hisat2/build/main.nf
View file

@ -11,7 +11,7 @@ process HISAT2_BUILD {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null) conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/rsem/preparereference/main.nf
View file

@ -9,7 +9,7 @@ process RSEM_PREPAREREFERENCE {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/salmon/index/main.nf
View file

@ -9,7 +9,7 @@ process SALMON_INDEX {
label "process_medium" label "process_medium"
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null) conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

2
software/star/genomegenerate/main.nf
View file

@ -9,7 +9,7 @@ process STAR_GENOMEGENERATE {
label 'process_high' label 'process_high'
publishDir "${params.outdir}", publishDir "${params.outdir}",
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', publish_id:'') }
// Note: 2.7X indices incompatible with AWS iGenomes. // Note: 2.7X indices incompatible with AWS iGenomes.
conda (params.enable_conda ? "bioconda::star=2.6.1d" : null) conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)

24
tests/software/bowtie/align/test.yml
View file

@ -8,17 +8,17 @@
- path: ./output/bowtie/test.bam - path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out - path: ./output/bowtie/test.out
md5sum: 4b9140ceadb8a18ae9330885370f8a0b md5sum: 4b9140ceadb8a18ae9330885370f8a0b
- path: ./output/bowtie/bowtie/test_genome.3.ebwt - path: ./output/index/bowtie/test_genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie/bowtie/test_genome.2.ebwt - path: ./output/index/bowtie/test_genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- path: ./output/bowtie/bowtie/test_genome.rev.2.ebwt - path: ./output/index/bowtie/test_genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459 md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- path: ./output/bowtie/bowtie/test_genome.4.ebwt - path: ./output/index/bowtie/test_genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie/bowtie/test_genome.rev.1.ebwt - path: ./output/index/bowtie/test_genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06 md5sum: b37aaf11853e65a3b13561f27a912b06
- path: ./output/bowtie/bowtie/test_genome.1.ebwt - path: ./output/index/bowtie/test_genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199 md5sum: d9b76ecf9fd0413240173273b38d8199
- name: bowtie align paired-end - name: bowtie align paired-end
@ -30,15 +30,15 @@
files: files:
- path: ./output/bowtie/test.bam - path: ./output/bowtie/test.bam
- path: ./output/bowtie/test.out - path: ./output/bowtie/test.out
- path: ./output/bowtie/bowtie/test_genome.3.ebwt - path: ./output/index/bowtie/test_genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie/bowtie/test_genome.2.ebwt - path: ./output/index/bowtie/test_genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- path: ./output/bowtie/bowtie/test_genome.rev.2.ebwt - path: ./output/index/bowtie/test_genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459 md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- path: ./output/bowtie/bowtie/test_genome.4.ebwt - path: ./output/index/bowtie/test_genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie/bowtie/test_genome.rev.1.ebwt - path: ./output/index/bowtie/test_genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06 md5sum: b37aaf11853e65a3b13561f27a912b06
- path: ./output/bowtie/bowtie/test_genome.1.ebwt - path: ./output/index/bowtie/test_genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199 md5sum: d9b76ecf9fd0413240173273b38d8199

12
tests/software/bowtie/build_test/test.yml
View file

@ -4,15 +4,15 @@
- bowtie - bowtie
- bowtie_build - bowtie_build
files: files:
- path: ./output/bowtie/bowtie/test_genome.3.ebwt - path: ./output/index/bowtie/test_genome.3.ebwt
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie/bowtie/test_genome.2.ebwt - path: ./output/index/bowtie/test_genome.2.ebwt
md5sum: 02b44af9f94c62ecd3c583048e25d4cf md5sum: 02b44af9f94c62ecd3c583048e25d4cf
- path: ./output/bowtie/bowtie/test_genome.rev.2.ebwt - path: ./output/index/bowtie/test_genome.rev.2.ebwt
md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459 md5sum: 9e6b0c4c1ddb99ae71ff8a4fe5ec6459
- path: ./output/bowtie/bowtie/test_genome.4.ebwt - path: ./output/index/bowtie/test_genome.4.ebwt
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie/bowtie/test_genome.rev.1.ebwt - path: ./output/index/bowtie/test_genome.rev.1.ebwt
md5sum: b37aaf11853e65a3b13561f27a912b06 md5sum: b37aaf11853e65a3b13561f27a912b06
- path: ./output/bowtie/bowtie/test_genome.1.ebwt - path: ./output/index/bowtie/test_genome.1.ebwt
md5sum: d9b76ecf9fd0413240173273b38d8199 md5sum: d9b76ecf9fd0413240173273b38d8199

24
tests/software/bowtie2/align/test.yml
View file

@ -7,17 +7,17 @@
files: files:
- path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/test_genome.3.bt2 - path: ./output/index/bowtie2/test_genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie2/bowtie2/test_genome.2.bt2 - path: ./output/index/bowtie2/test_genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/bowtie2/bowtie2/test_genome.1.bt2 - path: ./output/index/bowtie2/test_genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/bowtie2/bowtie2/test_genome.4.bt2 - path: ./output/index/bowtie2/test_genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/test_genome.rev.1.bt2 - path: ./output/index/bowtie2/test_genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184 md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/bowtie2/bowtie2/test_genome.rev.2.bt2 - path: ./output/index/bowtie2/test_genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597 md5sum: e3b4ef343dea4dd571642010a7d09597
- name: bowtie2 align paired-end - name: bowtie2 align paired-end
@ -29,15 +29,15 @@
files: files:
- path: ./output/bowtie2/test.bam - path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log - path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/bowtie2/test_genome.3.bt2 - path: ./output/index/bowtie2/test_genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie2/bowtie2/test_genome.2.bt2 - path: ./output/index/bowtie2/test_genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/bowtie2/bowtie2/test_genome.1.bt2 - path: ./output/index/bowtie2/test_genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/bowtie2/bowtie2/test_genome.4.bt2 - path: ./output/index/bowtie2/test_genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/test_genome.rev.1.bt2 - path: ./output/index/bowtie2/test_genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184 md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/bowtie2/bowtie2/test_genome.rev.2.bt2 - path: ./output/index/bowtie2/test_genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597 md5sum: e3b4ef343dea4dd571642010a7d09597

12
tests/software/bowtie2/build_test/test.yml
View file

@ -4,15 +4,15 @@
- bowtie2 - bowtie2
- bowtie2_build - bowtie2_build
files: files:
- path: ./output/bowtie2/bowtie2/test_genome.3.bt2 - path: ./output/index/bowtie2/test_genome.3.bt2
md5sum: 4ed93abba181d8dfab2e303e33114777 md5sum: 4ed93abba181d8dfab2e303e33114777
- path: ./output/bowtie2/bowtie2/test_genome.2.bt2 - path: ./output/index/bowtie2/test_genome.2.bt2
md5sum: 47b153cd1319abc88dda532462651fcf md5sum: 47b153cd1319abc88dda532462651fcf
- path: ./output/bowtie2/bowtie2/test_genome.1.bt2 - path: ./output/index/bowtie2/test_genome.1.bt2
md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf
- path: ./output/bowtie2/bowtie2/test_genome.4.bt2 - path: ./output/index/bowtie2/test_genome.4.bt2
md5sum: c25be5f8b0378abf7a58c8a880b87626 md5sum: c25be5f8b0378abf7a58c8a880b87626
- path: ./output/bowtie2/bowtie2/test_genome.rev.1.bt2 - path: ./output/index/bowtie2/test_genome.rev.1.bt2
md5sum: 52be6950579598a990570fbcf5372184 md5sum: 52be6950579598a990570fbcf5372184
- path: ./output/bowtie2/bowtie2/test_genome.rev.2.bt2 - path: ./output/index/bowtie2/test_genome.rev.2.bt2
md5sum: e3b4ef343dea4dd571642010a7d09597 md5sum: e3b4ef343dea4dd571642010a7d09597

10
tests/software/bwa/index/test.yml
View file

@ -4,13 +4,13 @@
- bwa - bwa
- bwa_index - bwa_index
files: files:
- path: ./output/bwa/bwa/test_genome.bwt - path: ./output/index/bwa/test_genome.bwt
md5sum: 0469c30a1e239dd08f68afe66fde99da md5sum: 0469c30a1e239dd08f68afe66fde99da
- path: ./output/bwa/bwa/test_genome.amb - path: ./output/index/bwa/test_genome.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/bwa/bwa/test_genome.sa - path: ./output/index/bwa/test_genome.sa
md5sum: ab3952cabf026b48cd3eb5bccbb636d1 md5sum: ab3952cabf026b48cd3eb5bccbb636d1
- path: ./output/bwa/bwa/test_genome.pac - path: ./output/index/bwa/test_genome.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwa/bwa/test_genome.ann - path: ./output/index/bwa/test_genome.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567

10
tests/software/bwamem2/index/test.yml
View file

@ -4,13 +4,13 @@
- bwamem2 - bwamem2
- bwamem2_index - bwamem2_index
files: files:
- path: ./output/bwamem2/bwamem2/test_genome.fasta.amb - path: ./output/index/bwamem2/test_genome.fasta.amb
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
- path: ./output/bwamem2/bwamem2/test_genome.fasta.pac - path: ./output/index/bwamem2/test_genome.fasta.pac
md5sum: 983e3d2cd6f36e2546e6d25a0da78d66 md5sum: 983e3d2cd6f36e2546e6d25a0da78d66
- path: ./output/bwamem2/bwamem2/test_genome.fasta.0123 - path: ./output/index/bwamem2/test_genome.fasta.0123
md5sum: b02870de80106104abcb03cd9463e7d8 md5sum: b02870de80106104abcb03cd9463e7d8
- path: ./output/bwamem2/bwamem2/test_genome.fasta.bwt.2bit.64 - path: ./output/index/bwamem2/test_genome.fasta.bwt.2bit.64
md5sum: d097a1b82dee375d41a1ea69895a9216 md5sum: d097a1b82dee375d41a1ea69895a9216
- path: ./output/bwamem2/bwamem2/test_genome.fasta.ann - path: ./output/index/bwamem2/test_genome.fasta.ann
md5sum: c32e11f6c859f166c7525a9c1d583567 md5sum: c32e11f6c859f166c7525a9c1d583567

12
tests/software/bwameth/index/test.yml
View file

@ -4,15 +4,15 @@
- bwameth - bwameth
- bwameth_index - bwameth_index
files: files:
- path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t
md5sum: 98039984526a41d04d6bd92fcc040c62 md5sum: 98039984526a41d04d6bd92fcc040c62
- path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.pac - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.pac
md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653 md5sum: 4d8e51cb0bbdeaf24576bdf0264d8653
- path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.amb - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.amb
md5sum: 249a4195069071ce47cd0bae68abe376 md5sum: 249a4195069071ce47cd0bae68abe376
- path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.ann - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.ann
md5sum: 46524d4359dcdfb203a235ab3b930dbb md5sum: 46524d4359dcdfb203a235ab3b930dbb
- path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.bwt - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.bwt
md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b md5sum: 84f65df7d42dbe84c9ccfaddfdd5ea6b
- path: ./output/bwameth/bwameth/test_genome.fasta.bwameth.c2t.sa - path: ./output/index/bwameth/test_genome.fasta.bwameth.c2t.sa
md5sum: d25f6486f5134f57ed5b258f6fbb8673 md5sum: d25f6486f5134f57ed5b258f6fbb8673

30
tests/software/salmon/index/test.yml
View file

@ -4,28 +4,28 @@
- salmon - salmon
- salmon_index - salmon_index
files: files:
- path: ./output/salmon/salmon/ref_indexing.log - path: ./output/index/salmon/ref_indexing.log
- path: ./output/salmon/salmon/refseq.bin - path: ./output/index/salmon/refseq.bin
md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7 md5sum: 79c4ddf34be3a98d5a7b9d153629a6f7
- path: ./output/salmon/salmon/versionInfo.json - path: ./output/index/salmon/versionInfo.json
md5sum: 204865f645102587c4953fccb256797c md5sum: 204865f645102587c4953fccb256797c
- path: ./output/salmon/salmon/complete_ref_lens.bin - path: ./output/index/salmon/complete_ref_lens.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08 md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/mphf.bin - path: ./output/index/salmon/mphf.bin
md5sum: 53669a47610e33e031faafd32703b714 md5sum: 53669a47610e33e031faafd32703b714
- path: ./output/salmon/salmon/pre_indexing.log - path: ./output/index/salmon/pre_indexing.log
- path: ./output/salmon/salmon/ctable.bin - path: ./output/index/salmon/ctable.bin
- path: ./output/salmon/salmon/duplicate_clusters.tsv - path: ./output/index/salmon/duplicate_clusters.tsv
md5sum: 51b5292e3a874119c0e1aa566e95d70c md5sum: 51b5292e3a874119c0e1aa566e95d70c
- path: ./output/salmon/salmon/reflengths.bin - path: ./output/index/salmon/reflengths.bin
md5sum: f57562f1fca3ae7b133f895ae13c3d08 md5sum: f57562f1fca3ae7b133f895ae13c3d08
- path: ./output/salmon/salmon/info.json - path: ./output/index/salmon/info.json
md5sum: 61ff4d3471134c280668355ddd39e99f md5sum: 61ff4d3471134c280668355ddd39e99f
- path: ./output/salmon/salmon/refAccumLengths.bin - path: ./output/index/salmon/refAccumLengths.bin
md5sum: 8d1970505b2b08ca0eb5ff7722b48cde md5sum: 8d1970505b2b08ca0eb5ff7722b48cde
- path: ./output/salmon/salmon/ctg_offsets.bin - path: ./output/index/salmon/ctg_offsets.bin
md5sum: 27a76542337df436436e66017f66dd25 md5sum: 27a76542337df436436e66017f66dd25
- path: ./output/salmon/salmon/rank.bin - path: ./output/index/salmon/rank.bin
md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71 md5sum: 3f34dca1ec26cdf89a6d19b1d1c07e71
- path: ./output/salmon/salmon/pos.bin - path: ./output/index/salmon/pos.bin
- path: ./output/salmon/salmon/seq.bin - path: ./output/index/salmon/seq.bin

27
tests/software/star/genomegenerate/test.yml
View file

@ -4,29 +4,28 @@
- star - star
- star_genomegenerate - star_genomegenerate
files: files:
- path: output/star/star/Genome - path: ./output/index/star/Genome
md5sum: 323c992bac354f93073ce0fc43f222f8 md5sum: 323c992bac354f93073ce0fc43f222f8
- path: output/star/star/SA - path: ./output/index/star/SA
md5sum: 3e70e4fc6d031e1915bb510727f2c559 md5sum: 3e70e4fc6d031e1915bb510727f2c559
- path: output/star/star/SAindex - path: ./output/index/star/SAindex
md5sum: a94198b95a245d4f64af2a7133b6ec7b md5sum: a94198b95a245d4f64af2a7133b6ec7b
- path: output/star/star/chrLength.txt - path: ./output/index/star/chrLength.txt
md5sum: f2bea3725fe1c01420c57fb73bdeb31a md5sum: f2bea3725fe1c01420c57fb73bdeb31a
- path: output/star/star/chrNameLength.txt - path: ./output/index/star/chrNameLength.txt
md5sum: c7ceb0a8827b2ea91c386933bee48742 md5sum: c7ceb0a8827b2ea91c386933bee48742
- path: output/star/star/chrStart.txt - path: ./output/index/star/chrStart.txt
md5sum: faf5c55020c99eceeef3e34188ac0d2f md5sum: faf5c55020c99eceeef3e34188ac0d2f
- path: output/star/star/exonGeTrInfo.tab - path: ./output/index/star/exonGeTrInfo.tab
md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6 md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
- path: output/star/star/exonInfo.tab - path: ./output/index/star/exonInfo.tab
md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343 md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
- path: output/star/star/genomeParameters.txt - path: ./output/index/star/sjdbInfo.txt
md5sum: 05e1041cbfb7f81686e17bc80b3ddcea
- path: output/star/star/sjdbInfo.txt
md5sum: 1082ab459363b3f2f7aabcef0979c1ed md5sum: 1082ab459363b3f2f7aabcef0979c1ed
- path: output/star/star/sjdbList.fromGTF.out.tab - path: ./output/index/star/sjdbList.fromGTF.out.tab
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/star/star/sjdbList.out.tab - path: ./output/index/star/sjdbList.out.tab
md5sum: d41d8cd98f00b204e9800998ecf8427e md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/star/star/transcriptInfo.tab - path: ./output/index/star/transcriptInfo.tab
md5sum: 8fbe69abbbef4f89da3854873984dbac md5sum: 8fbe69abbbef4f89da3854873984dbac
- path: ./output/index/star/genomeParameters.txt