Rearranging tests to test each module separately

.github/filters.yml

@@ -2,6 +2,35 @@ bandage_image:
   - software/bandage/image/**
   - tests/software/bandage/image/**
 
+bcftools_bgzip:
+  - software/bowtie/bgzip/**
+  - tests/software/bcftools/bgzip**
+
+bcftools_consensus:
+  - software/bowtie/bgzip/**
+  - software/bowtie/tabix/**
+  - software/bowtie/consesus/**
+  - tests/software/bcftools/consesus**
+
+bcftools_filter:
+  - software/bowtie/filter/**
+  - tests/software/bcftools/filter**
+
+bcftools_isec:
+  - software/bowtie/bgzip/**
+  - software/bowtie/tabix/**
+  - software/bowtie/isec/**
+  - tests/software/bcftools/isec**
+
+bcftools_stats:
+  - software/bowtie/stats/**
+  - tests/software/bcftools/stats**
+
+bcftools_tabix:
+  - software/bowtie/bgzip/**
+  - software/bowtie/tabix/**
+  - tests/software/bcftools/tabix**
+
 bowtie_align:
   - software/bowtie/align/**
   - software/bowtie/build/**

.github/workflows/bcftools_bgzip.yml

@@ -1,40 +0,0 @@
-name: bcftools_bgzip
-on:
-    push:
-        paths:
-            - software/bcftools/bgzip/**
-            - .github/workflows/bcftools_bgzip.yml
-            - tests/software/bcftools/**
-    pull_request:
-        paths:
-            - software/bcftools/bgzip/**
-            - .github/workflows/bcftools_bgzip.yml
-            - tests/software/bcftools/**
-
-jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
-        env:
-            NXF_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
-
-            - name: Install Nextflow
-              env:
-                  NXF_VER: ${{ matrix.nxf_version }}
-              run: |
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
-
-            - name: Set up Python
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.x"
-            - name: Install dependencies
-              run: python -m pip install --upgrade pip pytest-workflow
-
-            # Test the module
-            - run: pytest --tag bcftools_bgzip --symlink --wt 2

.github/workflows/bcftools_consensus.yml

@@ -1,44 +0,0 @@
-name: bcftools_consensus
-on:
-    push:
-        paths:
-            - software/bcftools/bgzip/**
-            - software/bcftools/tabix/**
-            - software/bcftools/consensus/**
-            - .github/workflows/bcftools_consensus.yml
-            - tests/software/bcftools/**
-    pull_request:
-        paths:
-            - software/bcftools/bgzip/**
-            - software/bcftools/tabix/**
-            - software/bcftools/consensus/**
-            - .github/workflows/bcftools_consensus.yml
-            - tests/software/bcftools/**
-
-jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
-        env:
-            NXF_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
-
-            - name: Install Nextflow
-              env:
-                  NXF_VER: ${{ matrix.nxf_version }}
-              run: |
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
-
-            - name: Set up Python
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.x"
-            - name: Install dependencies
-              run: python -m pip install --upgrade pip pytest-workflow
-
-            # Test the module
-            - run: pytest --tag bcftools_consensus --symlink --wt 2

.github/workflows/bcftools_filter.yml

@@ -1,40 +0,0 @@
-name: bcftools_filter
-on:
-    push:
-        paths:
-            - software/bcftools/filter/**
-            - .github/workflows/bcftools_filter.yml
-            - tests/software/bcftools/**
-    pull_request:
-        paths:
-            - software/bcftools/filter/**
-            - .github/workflows/bcftools_filter.yml
-            - tests/software/bcftools/**
-
-jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
-        env:
-            NXF_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
-
-            - name: Install Nextflow
-              env:
-                  NXF_VER: ${{ matrix.nxf_version }}
-              run: |
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
-
-            - name: Set up Python
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.x"
-            - name: Install dependencies
-              run: python -m pip install --upgrade pip pytest-workflow
-
-            # Test the module
-            - run: pytest --tag bcftools_filter --symlink --wt 2

.github/workflows/bcftools_isec.yml

@@ -1,44 +0,0 @@
-name: bcftools_isec
-on:
-    push:
-        paths:
-            - software/bcftools/bgzip/**
-            - software/bcftools/tabix/**
-            - software/bcftools/isec/**
-            - .github/workflows/bcftools_isec.yml
-            - tests/software/bcftools/**
-    pull_request:
-        paths:
-            - software/bcftools/bgzip/**
-            - software/bcftools/tabix/**
-            - software/bcftools/isec/**
-            - .github/workflows/bcftools_tabix.yml
-            - tests/software/bcftools/**
-
-jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
-        env:
-            NXF_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
-
-            - name: Install Nextflow
-              env:
-                  NXF_VER: ${{ matrix.nxf_version }}
-              run: |
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
-
-            - name: Set up Python
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.x"
-            - name: Install dependencies
-              run: python -m pip install --upgrade pip pytest-workflow
-
-            # Test the module
-            - run: pytest --tag bcftools_isec --symlink --wt 2

.github/workflows/bcftools_stats.yml

@@ -1,40 +0,0 @@
-name: bcftools_stats
-on:
-    push:
-        paths:
-            - software/bcftools/stats/**
-            - .github/workflows/bcftools_stats.yml
-            - tests/software/bcftools/**
-    pull_request:
-        paths:
-            - software/bcftools/stats/**
-            - .github/workflows/bcftools_stats.yml
-            - tests/software/bcftools/**
-
-jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
-        env:
-            NXF_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
-
-            - name: Install Nextflow
-              env:
-                  NXF_VER: ${{ matrix.nxf_version }}
-              run: |
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
-
-            - name: Set up Python
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.x"
-            - name: Install dependencies
-              run: python -m pip install --upgrade pip pytest-workflow
-
-            # Test the module
-            - run: pytest --tag bcftools_stats --symlink --wt 2

.github/workflows/bcftools_tabix.yml

@@ -1,42 +0,0 @@
-name: bcftools_tabix
-on:
-    push:
-        paths:
-            - software/bcftools/bgzip/**
-            - software/bcftools/tabix/**
-            - .github/workflows/bcftools_tabix.yml
-            - tests/software/bcftools/**
-    pull_request:
-        paths:
-            - software/bcftools/bgzip/**
-            - software/bcftools/tabix/**
-            - .github/workflows/bcftools_tabix.yml
-            - tests/software/bcftools/**
-
-jobs:
-    ci_test:
-        runs-on: ubuntu-latest
-        strategy:
-            matrix:
-                nxf_version: [20.11.0-edge]
-        env:
-            NXF_ANSI_LOG: false
-        steps:
-            - uses: actions/checkout@v2
-
-            - name: Install Nextflow
-              env:
-                  NXF_VER: ${{ matrix.nxf_version }}
-              run: |
-                  wget -qO- get.nextflow.io | bash
-                  sudo mv nextflow /usr/local/bin/
-
-            - name: Set up Python
-              uses: actions/setup-python@v2
-              with:
-                  python-version: "3.x"
-            - name: Install dependencies
-              run: python -m pip install --upgrade pip pytest-workflow
-
-            # Test the module
-            - run: pytest --tag bcftools_tabix --symlink --wt 2

tests/software/bcftools/bgzip/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_BGZIP } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
+
+workflow test_bcftools_bgzip {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+              file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+
+    BCFTOOLS_BGZIP ( input )
+}

tests/software/bcftools/bgzip/test.yml

@@ -0,0 +1,8 @@
+- name: Run bcftools bgzip test workflow
+  command: nextflow run ./tests/software/bcftools/bgzip -entry test_bcftools_bgzip -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools_bgzip
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: eb75ae1f08a1884f8edc59ed423471a2

tests/software/bcftools/consensus/main.nf

@@ -0,0 +1,23 @@
+#!/usr/bin/env nextflow
+
+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("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+    def fasta = []
+    fasta = Channel.of ([ [ id:'test' ], // meta map
+            file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ])
+
+    BCFTOOLS_BGZIP ( 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

@@ -0,0 +1,12 @@
+- name: Run bcftools consensus test workflow
+  command: nextflow run ./tests/software/bcftools/consensus -entry test_bcftools_consensus -c tests/config/nextflow.config
+  tags:
+    - 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

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+//keep --no-verson argument, otherwise md5 will change on each execution
+include { BCFTOOLS_FILTER } from '../../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] )
+
+workflow test_bcftools_filter {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+
+    BCFTOOLS_FILTER ( input )
+}

tests/software/bcftools/filter/test.yml

@@ -0,0 +1,8 @@
+- name: Run bcftools filter test workflow
+  command: nextflow run ./tests/software/bcftools/filter -entry test_bcftools_filter -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools_filter
+  files:
+    - path: output/bcftools/test.vcf.gz
+      md5sum: 16947ce72a127938d881113a1e6e696b

tests/software/bcftools/isec/main.nf

@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+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 = []
+
+    input1 = [ [ id:'test1' ], // meta map
+            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

@@ -0,0 +1,32 @@
+- name: Run bcftools isec test workflow
+  command: nextflow run ./tests/software/bcftools/isec -entry test_bcftools_isec -c tests/config/nextflow.config
+  tags:
+    - 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
+      md5sum: 8484b151ef902e25e54f7713d46ed90e
+    - path: output/bcftools/test/0001.vcf.gz
+      md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
+    - path: output/bcftools/test/0001.vcf.gz.tbi
+      md5sum: 8484b151ef902e25e54f7713d46ed90e
+    - path: output/bcftools/test/0002.vcf.gz
+      md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
+    - path: output/bcftools/test/0002.vcf.gz.tbi
+      md5sum: 8484b151ef902e25e54f7713d46ed90e
+    - path: output/bcftools/test/README.txt
+      md5sum: 306fcb71aafe414046a34bedd4d14304
+    - path: output/bcftools/test/sites.txt
+      md5sum: 01bb949ed7825ecf692bf0640e363647

tests/software/bcftools/main.nf

@@ -1,97 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-//keep arg of bcftools_filter, otherwise md5 will change on each execution
-include { BCFTOOLS_FILTER } from '../../../software/bcftools/filter/main.nf' addParams( options: ['args': '--no-version'] )
-include { BCFTOOLS_STATS } from '../../../software/bcftools/stats/main.nf' addParams( options: [:] )
-include { BCFTOOLS_BGZIP } from '../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
-include { BCFTOOLS_TABIX } from '../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
-include { BCFTOOLS_CONSENSUS } from '../../../software/bcftools/consensus/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_filter {
-
-    def input = []
-    input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
-
-    BCFTOOLS_FILTER ( input )
-}
-
-workflow test_bcftools_stats {
-
-    def input = []
-    input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
-
-    BCFTOOLS_STATS ( input )
-}
-
-workflow test_bcftools_bgzip {
-
-    def input = []
-    input = [ [ id:'test' ], // meta map
-              file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
-
-    BCFTOOLS_BGZIP ( input )
-}
-
-workflow test_bcftools_tabix {
-
-    def input = []
-    input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
-
-    BCFTOOLS_BGZIP ( input )
-    BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
-}
-
-workflow test_bcftools_consensus {
-
-    def input = []
-    input = [ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
-    def fasta = []
-    fasta = Channel.of ([ [ id:'test' ], // meta map
-            file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ])
-
-    BCFTOOLS_BGZIP ( input )
-    BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
-    BCFTOOLS_CONSENSUS ( BCFTOOLS_BGZIP.out.vcf
-                                    .join( BCFTOOLS_TABIX.out.tbi, by: [0] )
-                                    .join( fasta, by: [0] ) )
-}
-
-workflow test_bcftools_isec {
-
-    def input = []
-    input1 = [ [ id:'test1' ], // meta map
-            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 )
-    BCFTOOLS_ISEC   ( BCFTOOLS_BGZIP.out.vcf
-                        .mix( BCFTOOLS_TABIX.out.tbi )
-                        .mix( BCFTOOLS_BGZIP2.out.vcf )
-                        .mix( BCFTOOLS_TABIX2.out.tbi )
-                        .mix( BCFTOOLS_BGZIP3.out.vcf )
-                        .mix( BCFTOOLS_TABIX3.out.tbi)
-                        .map { [ it[1] ]}
-                        .collect()
-                        .map { [ [id: 'test'], it ] } )
-}

tests/software/bcftools/stats/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_STATS } from '../../../../software/bcftools/stats/main.nf' addParams( options: [:] )
+
+workflow test_bcftools_stats {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+
+    BCFTOOLS_STATS ( input )
+}

tests/software/bcftools/stats/test.yml

@@ -0,0 +1,8 @@
+- name: Run bcftools bgzip test workflow
+  command: nextflow run ./tests/software/bcftools/stats -entry test_bcftools_stats -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools_stats
+  files:
+    - path: output/bcftools/test.bcftools_stats.txt
+      md5sum: abfc6a90f84e24b2cc7e92cbce06200a

tests/software/bcftools/tabix/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+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: [:] )
+
+workflow test_bcftools_tabix {
+
+    def input = []
+    input = [ [ id:'test' ], // meta map
+            file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
+
+    BCFTOOLS_BGZIP ( input )
+    BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
+}

tests/software/bcftools/tabix/test.yml

@@ -0,0 +1,8 @@
+- name: Run bcftools tabix test workflow
+  command: nextflow run ./tests/software/bcftools/tabix -entry test_bcftools_tabix -c tests/config/nextflow.config
+  tags:
+    - bcftools
+    - bcftools_tabix
+  files:
+    - path: output/bcftools/test.vcf.gz.tbi
+      md5sum: 06d52177f819730dd409157914534e8d

tests/software/bcftools/test.yml

@@ -1,81 +0,0 @@
-- name: Run bcftools filter test workflow
-  command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_filter -c tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools_filter
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: 16947ce72a127938d881113a1e6e696b
-
-- name: Run bcftools stats test workflow
-  command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_stats -c tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools_stats
-  files:
-    - path: output/bcftools/test.bcftools_stats.txt
-      md5sum: abfc6a90f84e24b2cc7e92cbce06200a
-
-- name: Run bcftools bgzip test workflow
-  command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_bgzip -c tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools_bgzip
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: eb75ae1f08a1884f8edc59ed423471a2
-
-- name: Run bcftools tabix test workflow
-  command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_tabix -c tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools_tabix
-  files:
-    - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 06d52177f819730dd409157914534e8d
-
-- name: Run bcftools consensus test workflow
-  command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_consensus -c tests/config/nextflow.config
-  tags:
-    - 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
-
-- name: Run bcftools isec test workflow
-  command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_isec -c tests/config/nextflow.config
-  tags:
-    - 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
-      md5sum: 8484b151ef902e25e54f7713d46ed90e
-    - path: output/bcftools/test/0001.vcf.gz
-      md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
-    - path: output/bcftools/test/0001.vcf.gz.tbi
-      md5sum: 8484b151ef902e25e54f7713d46ed90e
-    - path: output/bcftools/test/0002.vcf.gz
-      md5sum: 4e84e3b6903fa44e8bd1acdeff9b265d
-    - path: output/bcftools/test/0002.vcf.gz.tbi
-      md5sum: 8484b151ef902e25e54f7713d46ed90e
-    - path: output/bcftools/test/README.txt
-      md5sum: 306fcb71aafe414046a34bedd4d14304
-    - path: output/bcftools/test/sites.txt
-      md5sum: 01bb949ed7825ecf692bf0640e363647