diff --git a/VerifyBamID/2.0.1--h32f71e1_2/VerifyBamID2.nf b/VerifyBamID/2.0.1--h32f71e1_2/VerifyBamID2.nf new file mode 100644 index 00000000..b185d3c3 --- /dev/null +++ b/VerifyBamID/2.0.1--h32f71e1_2/VerifyBamID2.nf @@ -0,0 +1,32 @@ +process VerifyBamID2 { + tag {"VerifyBamID2 ${sample_id}"} + label 'VERIFYBAMID_2_0_1_h32f71e1_2' + label 'VERIFYBAMID_2_0_1_h32f71e1_2_VerifyBamID2' + container = 'quay.io/biocontainers/verifybamid2:2.0.1--h32f71e1_2' + shell = ['/bin/bash', '-eo', 'pipefail'] + + input: + tuple (sample_id, path(bam), path(bai)) + + output: + tuple (sample_id, path("${output_prefix}.selfSM")) + + script: + output_prefix = "${sample_id}.contamination" + + """ + # creates a ${output_prefix}.selfSM file, a TSV file with 2 rows, 19 columns. + # First row are the keys (e.g., SEQ_SM, RG, FREEMIX), second row are the associated values + verifybamid2 \ + --Reference ${params.genome} \ + --BamFile ${bam} \ + --SVDPrefix ${params.contamination_path_prefix} \ + --UDPath ${params.contamination_sites_ud} \ + --MeanPath ${params.contamination_sites_mu} \ + --BedPath ${params.contamination_sites_bed} \ + --Verbose \ + --NumPC 4 \ + --NumThread ${task.cpus} \ + --Output ${output_prefix} + """ +}