<commit_before>// vim: ts=4:expandtab:sw=4:cindent
//////////////////////////////////////////////////////////////////
// 
// Pipeline stage to run cn.MOPs on exome data
//
//////////////////////////////////////////////////////////////////
cn_mops_call_cnvs = {

    var batch_name : false

    var prior_impact : 10,
        min_width : 5,
        lower_threshold : -0.8,
        upper_threshold: 0.55,
        panel_type: 'exome',
        norm_type: 0

    def outputFile = batch_name ? batch_name + '.cnmops.cnvs.tsv' : input.bam + '.cnmops.cnvs.tsv'
    def outputData = batch_name ? batch_name + '.cnmops.cnvs.tsv' : input.bam + '.cnmops.cnvs.RData'

    produce(outputFile, outputData) {
        R({"""

            source("$TOOLS/r-utils/cnv_utils.R")

            library(cn.mops)
            library(Rsamtools)

            bam.files = c('${inputs.bam.join("','")}')
<commit_msg>fix regression in cn mops pipeline<commit_after>// vim: ts=4:expandtab:sw=4:cindent
//////////////////////////////////////////////////////////////////
// 
// Pipeline stage to run cn.MOPs on exome data
//
//////////////////////////////////////////////////////////////////
cn_mops_call_cnvs = {

    var batch_name : false

    var prior_impact : 10,
        min_width : 5,
        lower_threshold : -0.8,
        upper_threshold: 0.55,
        panel_type: 'exome',
        norm_type: 0

    def outputFile = batch_name ? batch_name + '.cnmops.cnvs.tsv' : input.bam + '.cnmops.cnvs.tsv'
    def outputData = batch_name ? batch_name + '.cnmops.cnvs.RData' : input.bam + '.cnmops.cnvs.RData'

    produce(outputFile, outputData) {
        R({"""

            source("$TOOLS/r-utils/cnv_utils.R")

            library(cn.mops)
            library(Rsamtools)

            bam.files = c('${inputs.bam.join("','")}')

{'fraction_non_alphanumeric': 0.26933778519755147, 'fraction_numerical': 0.012242626599888704, 'mean_word_length': 1.4562841530054644, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6246779', 'n_tokens_mistral': 607, 'n_tokens_neox': 577, 'n_words': 105}