bwameth: pass genome index as directory

instead of single files

software/bwameth/align/main.nf

@@ -30,13 +30,12 @@ process BWAMETH_ALIGN {
     def software   = getSoftwareName(task.process)
     def prefix     = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
-    def c2t = index.first().toString() - '.bwameth' - '.c2t' - '.amb' - '.ann' - '.bwt' - '.pac' - '.sa'
     """
     bwameth.py \\
         $options.args \\
         $read_group \\
         -t $task.cpus \\
-        --reference $c2t \\
+        --reference ${index}/genome.fa \\
         $reads \\
         | samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
 

software/bwameth/align/meta.yml

@@ -52,9 +52,8 @@ input:
             List of input FastQ files of size 1 and 2 for single-end and paired-end data,
             respectively.
     - index:
-        type: file
+        type: dir
-        description: BWA genome index files
+        description: Directory containing bwameth genome index
-        pattern: "*.{amb,ann,bwt,pac,sa}"
     - fasta:
         type: file
         description: Input genome fasta file

software/bwameth/index/main.nf

@@ -19,11 +19,11 @@ process BWAMETH_INDEX {
     }
 
     input:
-    path fasta
+    path fasta, stageAs: "index/genome.fa"
 
     output:
-    path "*.bwameth.c2t*", emit: index
+    path "index"        , emit: index
-    path "*.version.txt" , emit: version
+    path "*.version.txt", emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/bwameth/index/meta.yml

@@ -42,9 +42,9 @@ input:
         description: Input genome fasta file
 output:
     - index:
-        type: file
+        type: dir
-        description: c2t converted genome BWA index files
+        description: Directory containing bwameth genome index
-        pattern: "*.{bwameth.c2t.amb,bwameth.c2t.ann,bwameth.c2t.bwt,bwameth.c2t.pac,bwameth.c2t.sa}"
+        pattern: "index"
     - version:
         type: file
         description: File containing software version

tests/software/bwameth/align/main.nf

@@ -11,20 +11,12 @@ include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../software/bwameth
 workflow test_bwameth_align_single_end {
 
     def input = []
-    def index = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true) ] ]
 
-    index = [ file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t",     checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.amb", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.ann", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.bwt", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.sa",  checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.pac", checkIfExists: true) ]
-
     BWAMETH_ALIGN_SE (
         input,
-        index
+        file("${launchDir}/tests/data/index/E_coli/bwameth", checkIfExists: true)
     )
 }
 
@@ -34,20 +26,12 @@ workflow test_bwameth_align_single_end {
 workflow test_bwameth_align_paired_end {
 
     def input = []
-    def index = []
     input = [ [ id:'test', single_end:false ], // meta map
               [ file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R1.fastq.gz", checkIfExists: true),
                 file("${launchDir}/tests/data/fastq/methylated_dna/Ecoli_10K_methylated_R2.fastq.gz", checkIfExists: true) ] ]
 
-    index = [ file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.amb", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.ann", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.bwt", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.sa", checkIfExists: true),
-              file("${launchDir}/tests/data/index/E_coli/bwameth/NC_010473.fa.bwameth.c2t.pac", checkIfExists: true) ]
-
     BWAMETH_ALIGN_PE (
         input,
-        index
+        file("${launchDir}/tests/data/index/E_coli/bwameth", checkIfExists: true)
     )
 }

tests/software/bwameth/align/test.yml

@@ -5,7 +5,7 @@
     - bwameth_align
   files:
     - path: output/test_single_end/test.bam
-      md5sum: d56665d96a0ebb8e739ae41af8a37181
+      md5sum: 48dde56f7b74de3a3e0b1914c45150de
 
 - name: Run bwameth paired-end test workflow
   command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
@@ -14,4 +14,4 @@
     - bwameth_align
   files:
     - path: output/test_paired_end/test.bam
-      md5sum: 58b918ddddc09866e13a1a45f22e7434
+      md5sum: b473343b32b7cfc677bfad1ab0e6bb5a

tests/software/bwameth/index/test.yml

@@ -4,15 +4,15 @@
     - bwameth
     - bwameth_index
   files:
-    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.pac
+    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.pac
       md5sum: 7586c6a3be45c4dea15376a5c7bb9bf0
-    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.amb
+    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.amb
       md5sum: 87e019665cbb66bdee2bacccb26845c9
-    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.ann
+    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.ann
       md5sum: a4659a63572b6998c67457bd8e95790d
-    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.bwt
+    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.bwt
       md5sum: 582854008bcbe99d5b51290773a7db5f
-    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t
+    - path: ./output/bwameth/index/genome.fa.bwameth.c2t
       md5sum: db670853725f4a31080c991e9df6b330
-    - path: ./output/bwameth/NC_010473.fa.bwameth.c2t.sa
+    - path: ./output/bwameth/index/genome.fa.bwameth.c2t.sa
       md5sum: 020db07e7e1544dc961c30c9936f3213