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Merge pull request #242 from MaxUlysse/germline
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Code polishing + add BWAMEM2_MEM process
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@FriederikeHanssen
FriederikeHanssen authored Jul 16, 2020
2 parents aa4d103 + 131cd74 commit 216b529
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Showing 19 changed files with 544 additions and 558 deletions.
6 changes: 3 additions & 3 deletions lib/Headers.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ class Headers {
static String nf_core(workflow, monochrome_logs) {
Map colors = log_colours(monochrome_logs)
String.format(
"""\n
-${colors.dim}----------------------------------------------------${colors.reset}-
"""
-${colors.dim}----------------------------------------------------${colors.reset}-
${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset}
${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset}
Expand All @@ -39,7 +39,7 @@ class Headers {
${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
-${colors.dim}--------------------------------------------------${colors.reset}-
""".stripIndent()
""".stripIndent()
)
}
}
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121 changes: 110 additions & 11 deletions lib/Schema.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -82,31 +82,130 @@ class JSON {
def Map summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = run_name ?: workflow.runName
// TODO nf-core: Report custom parameters here
summary['Input'] = params.input
summary['Fasta File'] = params.fasta
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"

summary['Input'] = params.input
// summary['Step'] = step
summary['Genome'] = params.genome
// if (params.no_intervals && step != 'annotate') summary['Intervals'] = 'Do not use'
summary['Nucleotides/s'] = params.nucleotides_per_second
if (params.sentieon) summary['Sention'] = "Using Sentieon for Preprocessing and/or Variant Calling"
// if (params.skip_qc) summary['QC tools skipped'] = skip_qc.join(', ')
if (params.target_bed) summary['Target BED'] = params.target_bed
// if (params.tools) summary['Tools'] = tools.join(', ')
if (params.trim_fastq || params.split_fastq) summary['Modify fastqs'] = "trim and/or split"

if (params.trim_fastq) {
summary['Fastq trim'] = "Fastq trim selected"
summary['Trim R1'] = "${params.clip_r1} bp"
summary['Trim R2'] = "${params.clip_r2} bp"
summary["Trim 3 R1"] = "${params.three_prime_clip_r1} bp"
summary["Trim 3 R2"] = "${params.three_prime_clip_r2} bp"
summary['NextSeq Trim'] = "${params.trim_nextseq} bp"
summary['Saved Trimmed Fastq'] = params.save_trimmed ? 'Yes' : 'No'
}
if (params.split_fastq) summary['Reads in fastq'] = params.split_fastq

summary['MarkDuplicates'] = "Options"
summary['Java options'] = params.markdup_java_options
summary['GATK Spark'] = params.no_gatk_spark ? 'No' : 'Yes'

summary['Save BAMs mapped'] = params.save_bam_mapped ? 'Yes' : 'No'
summary['Skip MarkDuplicates'] = params.skip_markduplicates ? 'Yes' : 'No'

// if ('ascat' in tools) {
summary['ASCAT'] = "Options"
if (params.ascat_purity) summary['purity'] = params.ascat_purity
if (params.ascat_ploidy) summary['ploidy'] = params.ascat_ploidy
// }

// if ('controlfreec' in tools) {
summary['Control-FREEC'] = "Options"
if (params.cf_window) summary['window'] = params.cf_window
if (params.cf_coeff) summary['coeff of variation'] = params.cf_coeff
if (params.cf_ploidy) summary['ploidy'] = params.cf_ploidy
// }

// if ('haplotypecaller' in tools) summary['GVCF'] = params.no_gvcf ? 'No' : 'Yes'
// if ('strelka' in tools && 'manta' in tools) summary['Strelka BP'] = params.no_strelka_bp ? 'No' : 'Yes'
// if (params.pon && ('mutect2' in tools || (params.sentieon && 'tnscope' in tools))) summary['Panel of normals'] = params.pon

// if (params.annotate_tools) summary['Tools to annotate'] = annotate_tools.join(', ')

if (params.annotation_cache) {
summary['Annotation cache'] = "Enabled"
if (params.snpeff_cache) summary['snpEff cache'] = params.snpeff_cache
if (params.vep_cache) summary['VEP cache'] = params.vep_cache
}

if (params.cadd_cache) {
summary['CADD cache'] = "Enabled"
if (params.cadd_indels) summary['CADD indels'] = params.cadd_indels
if (params.cadd_wg_snvs) summary['CADD wg snvs'] = params.cadd_wg_snvs
}

if (params.genesplicer) summary['genesplicer'] = "Enabled"

if (params.igenomes_base && !params.igenomes_ignore) summary['AWS iGenomes base'] = params.igenomes_base
if (params.igenomes_ignore) summary['AWS iGenomes'] = "Do not use"
if (params.genomes_base && !params.igenomes_ignore) summary['Genomes base'] = params.genomes_base

summary['Save Reference'] = params.save_reference ? 'Yes' : 'No'

if (params.ac_loci) summary['Loci'] = params.ac_loci
if (params.ac_loci_gc) summary['Loci GC'] = params.ac_loci_gc
if (params.bwa) summary['BWA indexes'] = params.bwa
if (params.chr_dir) summary['Chromosomes'] = params.chr_dir
if (params.chr_length) summary['Chromosomes length'] = params.chr_length
if (params.dbsnp) summary['dbsnp'] = params.dbsnp
if (params.dbsnp_index) summary['dbsnp index'] = params.dbsnp_index
if (params.dict) summary['dict'] = params.dict
if (params.fasta) summary['fasta reference'] = params.fasta
if (params.fasta_fai) summary['fasta index'] = params.fasta_fai
if (params.germline_resource) summary['germline resource'] = params.germline_resource
if (params.germline_resource_index) summary['germline resource index'] = params.germline_resource_index
if (params.intervals) summary['intervals'] = params.intervals
if (params.known_indels) summary['known indels'] = params.known_indels
if (params.known_indels_index) summary['known indels index'] = params.known_indels_index
if (params.mappability) summary['Mappability'] = params.mappability
if (params.snpeff_cache) summary['snpEff cache'] = params.snpeff_cache
if (params.snpeff_db) summary['snpEff DB'] = params.snpeff_db
if (params.species) summary['snpEff species'] = params.species
if (params.vep_cache) summary['VEP cache'] = params.vep_cache
if (params.vep_cache_version) summary['VEP cache version'] = params.vep_cache_version

summary['Output dir'] = params.outdir
summary['Publish dir mode'] = params.publish_dir_mode
if (params.sequencing_center) summary['Sequenced by'] = params.sequencing_center

summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
summary['Script dir'] = workflow.projectDir
summary['User'] = workflow.userName
if (workflow.profile.contains('awsbatch')) {
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
summary['AWS CLI'] = params.awscli
}

if (params.multiqc_config) summary['MultiQC config'] = params.multiqc_config

summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Descr'] = params.config_profile_description
if (params.config_profile_contact) summary['Config Profile Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['Config Profile URL'] = params.config_profile_url

if (params.config_profile_description) summary['Description'] = params.config_profile_description
if (params.config_profile_contact) summary['Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['URL'] = params.config_profile_url

summary['Config Files'] = workflow.configFiles.join(', ')

if (params.email || params.email_on_fail) {
summary['E-mail Address'] = params.email
summary['E-mail on failure'] = params.email_on_fail
summary['MultiQC maxsize'] = params.max_multiqc_email_size
}

if (workflow.profile.contains('awsbatch')) {
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
summary['AWS CLI'] = params.awscli
}

return summary
}

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