Separate test data to break dependencies between bcftools modules tests

.github/filters.yml

@@ -7,8 +7,6 @@ bcftools_bgzip:
   - tests/software/bcftools/bgzip**
 
 bcftools_consensus:
-  - software/bowtie/bgzip/**
-  - software/bowtie/tabix/**
   - software/bowtie/consesus/**
   - tests/software/bcftools/consesus**
 
@@ -17,8 +15,6 @@ bcftools_filter:
   - tests/software/bcftools/filter**
 
 bcftools_isec:
-  - software/bowtie/bgzip/**
-  - software/bowtie/tabix/**
   - software/bowtie/isec/**
   - tests/software/bcftools/isec**
 
@@ -27,7 +23,6 @@ bcftools_stats:
   - tests/software/bcftools/stats**
 
 bcftools_tabix:
-  - software/bowtie/bgzip/**
   - software/bowtie/tabix/**
   - tests/software/bcftools/tabix**
 

tests/software/bcftools/bgzip/main.nf

@@ -8,7 +8,7 @@ workflow test_bcftools_bgzip {
 
     def input = []
     input = [ [ id:'test' ], // meta map
-              file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+              [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]]
 
     BCFTOOLS_BGZIP ( input )
 }

tests/software/bcftools/consensus/main.nf

@@ -2,22 +2,15 @@
 
 nextflow.enable.dsl = 2
 
-include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
-include { BCFTOOLS_TABIX as BCFTOOLS_TABIX } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
 include { BCFTOOLS_CONSENSUS as BCFTOOLS_CONSENSUS } from '../../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
 
 workflow test_bcftools_consensus {
 
     def input = []
     input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+              [ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ],
-    def fasta = []
+              [ file("${launchDir}/tests/data/vcf/test.vcf.gz.tbi", checkIfExists: true) ],
-    fasta = Channel.of ([ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ] ]
-            file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ])
 
-    BCFTOOLS_BGZIP ( input )
+    BCFTOOLS_CONSENSUS ( input )
-    BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
-    BCFTOOLS_CONSENSUS ( BCFTOOLS_BGZIP.out.vcf
-                                    .join( BCFTOOLS_TABIX.out.tbi, by: [0] )
-                                    .join( fasta, by: [0] ) )
 }

tests/software/bcftools/consensus/test.yml

@@ -4,9 +4,5 @@
     - bcftools
     - bcftools_consensus
   files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: eb75ae1f08a1884f8edc59ed423471a2
-    - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 06d52177f819730dd409157914534e8d
     - path: output/bcftools/test.fa
       md5sum: c9e7ac4537756a0b33bcf17117f9a065

tests/software/bcftools/filter/main.nf

@@ -9,7 +9,7 @@ workflow test_bcftools_filter {
 
     def input = []
     input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+              [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]]
 
     BCFTOOLS_FILTER ( input )
 }

tests/software/bcftools/isec/main.nf

@@ -2,43 +2,19 @@
 
 nextflow.enable.dsl = 2
 
-include { BCFTOOLS_BGZIP } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
-include { BCFTOOLS_TABIX } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
 include { BCFTOOLS_ISEC } from '../../../../software/bcftools/isec/main.nf' addParams( options: ['args': '--nfiles +2 --output-type z --no-version'] )
-include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP2 } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
-include { BCFTOOLS_TABIX as BCFTOOLS_TABIX2 } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
-include { BCFTOOLS_BGZIP as BCFTOOLS_BGZIP3 } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
-include { BCFTOOLS_TABIX as BCFTOOLS_TABIX3 } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
 
 workflow test_bcftools_isec {
 
-    def input1, input2, input3 = []
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              [ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true)],
+              [ file("${launchDir}/tests/data/vcf/test.vcf.gz.tbi", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test2.vcf.gz.tbi", checkIfExists: true),
+                file("${launchDir}/tests/data/vcf/test3.vcf.gz.tbi", checkIfExists: true) ]]
 
-    input1 = [ [ id:'test1' ], // meta map
+    BCFTOOLS_ISEC ( input )
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
 
-    input2 = [ [ id:'test2' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
-
-    input3 = [ [ id:'test3' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
-
-    BCFTOOLS_BGZIP  ( input1 )
-    BCFTOOLS_TABIX  ( BCFTOOLS_BGZIP.out.vcf )
-    BCFTOOLS_BGZIP2 ( input2 )
-    BCFTOOLS_TABIX2 ( BCFTOOLS_BGZIP2.out.vcf )
-    BCFTOOLS_BGZIP3 ( input3 )
-    BCFTOOLS_TABIX3 ( BCFTOOLS_BGZIP3.out.vcf )
-
-    vcfs = BCFTOOLS_BGZIP.out.vcf
-                        .mix( BCFTOOLS_BGZIP2.out.vcf )
-                        .mix( BCFTOOLS_BGZIP3.out.vcf )
-                        .map { [ it[1] ]}.collect().map { [ [id: 'test'], it ] }
-
-    tbis = BCFTOOLS_TABIX.out.tbi
-                        .mix( BCFTOOLS_TABIX2.out.tbi )
-                        .mix( BCFTOOLS_TABIX3.out.tbi )
-                        .map { [ it[1] ]}.collect().map { [ [id: 'test'], it ] }
-
-    BCFTOOLS_ISEC ( vcfs.join(tbis) )
 }

tests/software/bcftools/isec/test.yml

@@ -4,16 +4,6 @@
     - bcftools
     - bcftools_isec
   files:
-    - path: output/bcftools/test1.vcf.gz
-      md5sum: eb75ae1f08a1884f8edc59ed423471a2
-    - path: output/bcftools/test1.vcf.gz.tbi
-      md5sum: 06d52177f819730dd409157914534e8d
-    - path: output/bcftools/test2.vcf.gz
-      md5sum: eb75ae1f08a1884f8edc59ed423471a2
-    - path: output/bcftools/test2.vcf.gz.tbi
-      md5sum: 06d52177f819730dd409157914534e8d
-    - path: output/bcftools/test3.vcf.gz
-      md5sum: eb75ae1f08a1884f8edc59ed423471a2
     - path: output/bcftools/test/0000.vcf.gz
       md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
     - path: output/bcftools/test/0000.vcf.gz.tbi
@@ -27,6 +17,6 @@
     - path: output/bcftools/test/0002.vcf.gz.tbi
       md5sum: 8484b151ef902e25e54f7713d46ed90e
     - path: output/bcftools/test/README.txt
-      md5sum: 306fcb71aafe414046a34bedd4d14304
+      md5sum: 63ef64134d2685bc5d50332ef20389d2
     - path: output/bcftools/test/sites.txt
       md5sum: 01bb949ed7825ecf692bf0640e363647

tests/software/bcftools/stats/main.nf

@@ -8,7 +8,7 @@ workflow test_bcftools_stats {
 
     def input = []
     input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+              [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]]
 
     BCFTOOLS_STATS ( input )
 }

tests/software/bcftools/tabix/main.nf

@@ -9,8 +9,7 @@ workflow test_bcftools_tabix {
 
     def input = []
     input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+              [ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ]
 
-    BCFTOOLS_BGZIP ( input )
+    BCFTOOLS_TABIX ( input )
-    BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
 }