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

* 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

software/bowtie/build/main.nf

@@ -9,7 +9,7 @@ process BOWTIE_BUILD {
     label 'process_high'
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/bowtie2/build/main.nf

@@ -9,7 +9,7 @@ process BOWTIE2_BUILD {
     label 'process_high'
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/bwa/index/main.nf

@@ -9,7 +9,7 @@ process BWA_INDEX {
     label 'process_high'
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/bwamem2/index/main.nf

@@ -9,7 +9,7 @@ process BWAMEM2_INDEX {
     label 'process_high'
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/bwameth/index/main.nf

@@ -9,7 +9,7 @@ process BWAMETH_INDEX {
     label 'process_high'
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/hisat2/build/main.nf

@@ -11,7 +11,7 @@ process HISAT2_BUILD {
     label 'process_high'
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/rsem/preparereference/main.nf

@@ -9,7 +9,7 @@ process RSEM_PREPAREREFERENCE {
     label 'process_high'
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/salmon/index/main.nf

@@ -9,7 +9,7 @@ process SALMON_INDEX {
     label "process_medium"
     publishDir "${params.outdir}",
         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)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

software/star/genomegenerate/main.nf

@@ -9,7 +9,7 @@ process STAR_GENOMEGENERATE {
     label 'process_high'
     publishDir "${params.outdir}",
         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.
     conda (params.enable_conda ? "bioconda::star=2.6.1d" : null)

tests/software/bowtie/align/test.yml

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

tests/software/bowtie/build_test/test.yml

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

tests/software/bowtie2/align/test.yml

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

tests/software/bowtie2/build_test/test.yml

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

tests/software/bwa/index/test.yml

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

tests/software/bwamem2/index/test.yml

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

tests/software/bwameth/index/test.yml

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

tests/software/salmon/index/test.yml

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

tests/software/star/genomegenerate/test.yml

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