added star genomegenerate test

.github/workflows/star_genomegenerate.yml

@@ -0,0 +1,40 @@
+name: star_genomegenerate
+on:
+  push:
+    paths:
+      - software/star/genomegenerate/**
+      - .github/workflows/star_genomegenerate.yml
+      - tests/software/star/**
+  pull_request:
+    paths:
+      - software/star/index/**
+      - .github/workflows/star_genomegenerate.yml
+      - tests/software/star/**
+
+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 star_genomegenerate --symlink --wt 2

tests/software/star/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STAR_ALIGN } from '../../../software/star/align/main.nf' addParams( options: [:] )
+include { STAR_GENOMEGENERATE } from '../../../software/star/genomegenerate/main.nf'  addParams( options: [:] )
+
+workflow test_star_genomegenerate {
+    fasta = file("${launchDir}/tests/data/fasta/E_coli/GCF_000019425.1_ASM1942v1_genomic.fna", checkIfExists: true)
+    gtf = file("${launchDir}/tests/data/gff/GCF_000019425.1_ASM1942v1_genomic.gtf", checkIfExists: true)
+    STAR_GENOMEGENERATE ( fasta, gtf )
+}
+
+// workflow test_star_alignment_single_end {
+
+//     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+//     BOWTIE_INDEX ( fasta )
+
+//     def input = []
+//     input = [ [ id:'test', single_end:true ], // meta map
+//               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true) ] ]
+//     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
+// }
+
+// workflow test_star_alignment_paired_end {
+//     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
+//     BOWTIE_INDEX ( fasta )
+
+//     def input = []
+//     input = [ [ id:'test', single_end:false ], // meta map
+//               [ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
+//                 file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
+//     BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
+// }

tests/software/star/test.yml

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+- name: Run star genomegenerate
+  command: nextflow run ./tests/software/star -profile docker -entry test_star_genomegenerate -c tests/config/nextflow.config
+  tags:
+    - star
+    - star_genomegenerate
+  files:
+    - path: output/star/star/Genome
+      md5sum: 323c992bac354f93073ce0fc43f222f8
+    - path: output/star/star/SA
+      md5sum: 3e70e4fc6d031e1915bb510727f2c559
+    - path: output/star/star/SAindex
+      md5sum: 05a7baf30bda37f42f9fcf187a6e8247
+    - path: output/star/star/chrLength.txt
+      md5sum: f2bea3725fe1c01420c57fb73bdeb31a
+    - path: output/star/star/chrNameLength.txt
+      md5sum: c7ceb0a8827b2ea91c386933bee48742
+    - path: output/star/star/chrStart.txt
+      md5sum: faf5c55020c99eceeef3e34188ac0d2f
+
+    - path: output/star/star/exonGeTrInfo.tab
+      md5sum: aec6e7a1ae3fc8c638ce5a9ce9c886b6
+    - path: output/star/star/exonInfo.tab
+      md5sum: 42eca6ebc2dc72d9d6e6b3acd3714343
+    - path: output/star/star/genomeParameters.txt
+      md5sum: ba83e83fc204d48534a1bb11f378076c
+    - path: output/star/star/sjdbInfo.txt
+      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
+    - path: output/star/star/sjdbList.fromGTF.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/sjdbList.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/star/star/transcriptInfo.tab
+      md5sum: 8fbe69abbbef4f89da3854873984dbac