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

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* 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
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19 changed files with 93 additions and 94 deletions
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6
README.md
View file

@ -11,7 +11,7 @@
[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core) [![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)
[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) [![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
> THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE! > THIS REPOSITORY IS UNDER ACTIVE DEVELOPMENT. SYNTAX, ORGANISATION AND LAYOUT MAY CHANGE WITHOUT NOTICE!
> PLEASE BE KIND TO OUR CODE REVIEWERS AND SUBMIT ONE PULL REQUEST PER MODULE :) > PLEASE BE KIND TO OUR CODE REVIEWERS AND SUBMIT ONE PULL REQUEST PER MODULE :)
A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation. A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) module files containing tool-specific process definitions and their associated documentation.
@ -42,7 +42,7 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
```console ```console
$ nf-core modules list $ nf-core modules list
,--./,-. ,--./,-.
___ __ __ __ ___ /,-._.--~\ ___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } { |\ | |__ __ / ` / \ |__) |__ } {
@ -306,7 +306,7 @@ In order to test that each module added to `nf-core/modules` is actually working
### Running tests manually ### Running tests manually
As outlined in the [nf-core modules create](#nf-core-modules-create) section we have made it quite trivial to create an initial yaml file (via the `nf-core modules create-test-yml` command) containing a listing of all of the module output files and their associated md5sums. However, md5sum checks may not be appropriate for all output files if for example they contain timestamps. This is why it is a good idea to re-run the tests locally with `pytest-workflow` before you create your pull request adding the module. If your files do indeed have timestamps or other issues that prevent you from using the md5sum check, then you can edit the `test.yml` file to instead check that the file contains some specific content or as a last resort, if it exists. The different test options are listed in the [pytest-workflow docs](https://pytest-workflow.readthedocs.io/en/stable/#test-options). As outlined in the [nf-core modules create](#nf-core-modules-create) section we have made it quite trivial to create an initial yaml file (via the `nf-core modules create-test-yml` command) containing a listing of all of the module output files and their associated md5sums. However, md5sum checks may not be appropriate for all output files if for example they contain timestamps. This is why it is a good idea to re-run the tests locally with `pytest-workflow` before you create your pull request adding the module. If your files do indeed have timestamps or other issues that prevent you from using the md5sum check, then you can edit the `test.yml` file to instead check that the file contains some specific content or as a last resort, if it exists. The different test options are listed in the [pytest-workflow docs](https://pytest-workflow.readthedocs.io/en/stable/#test-options).
Please follow the steps below to run the tests locally: Please follow the steps below to run the tests locally:

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
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@ -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
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@ -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

29
tests/software/star/genomegenerate/test.yml
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@ -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