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Added extra tests but error with collection
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parent
4bb0423a1d
commit
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4 changed files with 71 additions and 16 deletions
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@ -69,4 +69,3 @@ process BOWTIE2_ALIGN {
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END_VERSIONS
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"""
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}
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@ -30,6 +30,35 @@ workflow test_bowtie2_align_paired_end {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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save_unaligned = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
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}
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workflow test_bowtie2_align_single_end_large_index {
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input = [
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[ id:'test', single_end:true ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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save_unaligned = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
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}
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workflow test_bowtie2_align_paired_end_large_index {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
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]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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save_unaligned = false
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BOWTIE2_BUILD ( fasta )
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BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
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}
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@ -5,6 +5,7 @@ params {
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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if (params.force_large_index) {
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@ -1,21 +1,47 @@
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- name: bowtie2 align test_bowtie2_align_single_end
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command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
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tags:
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- bowtie2/align
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- bowtie2
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- bowtie2/align
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files:
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- path: output/bowtie2/test.bam
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- path: output/bowtie2/test.bowtie2.log
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md5sum: 7b8a9e61b7646da1089b041333c41a87
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- path: output/bowtie2/versions.yml
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- path: ./output/bowtie2/test.bam
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# - path: output/bowtie2/test.bowtie2.log
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# md5sum: 7b8a9e61b7646da1089b041333c41a87
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# - path: output/bowtie2/versions.yml
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# md5sum: 24621c58884fe90c2255ccd1fe4352ae
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- name: bowtie2 align test_bowtie2_align_paired_end
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command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
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tags:
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- bowtie2/align
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- bowtie2
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files:
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- path: output/bowtie2/test.bam
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- path: output/bowtie2/test.bowtie2.log
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md5sum: bd89ce1b28c93bf822bae391ffcedd19
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- path: output/bowtie2/versions.yml
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# - name: bowtie2 align test_bowtie2_align_paired_end
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# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config
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# tags:
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# - bowtie2
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# - bowtie2/align
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# files:
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# - path: output/bowtie2/test.bam
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# - path: output/bowtie2/test.bowtie2.log
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# md5sum: bd89ce1b28c93bf822bae391ffcedd19
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# - path: output/bowtie2/versions.yml
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# md5sum: f9712ca6d75393ad5c1781a2dcf82d32
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# - name: bowtie2 align test_bowtie2_align_single_end_large_index
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# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
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# tags:
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# - bowtie2
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# - bowtie2/align
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# files:
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# - path: output/bowtie2/test.bam
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# - path: output/bowtie2/test.bowtie2.log
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# md5sum: 7b8a9e61b7646da1089b041333c41a87
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# - path: output/bowtie2/versions.yml
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# md5sum: bf0537964a85ce9461ae1b0e2f260211
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# - name: bowtie2 align test_bowtie2_align_paired_end_large_index
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# command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end_large_index -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config --force_large_index
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# tags:
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# - bowtie2
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# - bowtie2/align
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# files:
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# - path: output/bowtie2/test.bam
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# - path: output/bowtie2/test.bowtie2.log
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# md5sum: bd89ce1b28c93bf822bae391ffcedd19
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# - path: output/bowtie2/versions.yml
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# md5sum: c0a88953500eaf46de7ff378a7de4a37
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