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FriederikeHanssenFriederikeHanssen
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Merge pull request #242 from MaxUlysse/germline
Code polishing + add BWAMEM2_MEM process
2 parents aa4d103 + 131cd74 commit 216b529

19 files changed

+544
-558
lines changed

‎lib/Headers.groovy‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -23,8 +23,8 @@ class Headers {
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static String nf_core(workflow, monochrome_logs) {
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Map colors = log_colours(monochrome_logs)
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String.format(
26-
"""\n
27-
-${colors.dim}----------------------------------------------------${colors.reset}-
26+
"""
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-${colors.dim}----------------------------------------------------${colors.reset}-
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${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
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${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset}
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${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset}
@@ -39,7 +39,7 @@ class Headers {
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${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
4141
-${colors.dim}--------------------------------------------------${colors.reset}-
42-
""".stripIndent()
42+
""".stripIndent()
4343
)
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}
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}

‎lib/Schema.groovy‎

Lines changed: 110 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -82,31 +82,130 @@ class JSON {
8282
def Map summary = [:]
8383
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
8484
summary['Run Name'] = run_name ?: workflow.runName
85-
// TODO nf-core: Report custom parameters here
86-
summary['Input'] = params.input
87-
summary['Fasta File'] = params.fasta
8885
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
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if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
87+
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summary['Input'] = params.input
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// summary['Step'] = step
90+
summary['Genome'] = params.genome
91+
// if (params.no_intervals && step != 'annotate') summary['Intervals'] = 'Do not use'
92+
summary['Nucleotides/s'] = params.nucleotides_per_second
93+
if (params.sentieon) summary['Sention'] = "Using Sentieon for Preprocessing and/or Variant Calling"
94+
// if (params.skip_qc) summary['QC tools skipped'] = skip_qc.join(', ')
95+
if (params.target_bed) summary['Target BED'] = params.target_bed
96+
// if (params.tools) summary['Tools'] = tools.join(', ')
97+
if (params.trim_fastq || params.split_fastq) summary['Modify fastqs'] = "trim and/or split"
98+
99+
if (params.trim_fastq) {
100+
summary['Fastq trim'] = "Fastq trim selected"
101+
summary['Trim R1'] = "${params.clip_r1} bp"
102+
summary['Trim R2'] = "${params.clip_r2} bp"
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summary["Trim 3 R1"] = "${params.three_prime_clip_r1} bp"
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summary["Trim 3 R2"] = "${params.three_prime_clip_r2} bp"
105+
summary['NextSeq Trim'] = "${params.trim_nextseq} bp"
106+
summary['Saved Trimmed Fastq'] = params.save_trimmed ? 'Yes' : 'No'
107+
}
108+
if (params.split_fastq) summary['Reads in fastq'] = params.split_fastq
109+
110+
summary['MarkDuplicates'] = "Options"
111+
summary['Java options'] = params.markdup_java_options
112+
summary['GATK Spark'] = params.no_gatk_spark ? 'No' : 'Yes'
113+
114+
summary['Save BAMs mapped'] = params.save_bam_mapped ? 'Yes' : 'No'
115+
summary['Skip MarkDuplicates'] = params.skip_markduplicates ? 'Yes' : 'No'
116+
117+
// if ('ascat' in tools) {
118+
summary['ASCAT'] = "Options"
119+
if (params.ascat_purity) summary['purity'] = params.ascat_purity
120+
if (params.ascat_ploidy) summary['ploidy'] = params.ascat_ploidy
121+
// }
122+
123+
// if ('controlfreec' in tools) {
124+
summary['Control-FREEC'] = "Options"
125+
if (params.cf_window) summary['window'] = params.cf_window
126+
if (params.cf_coeff) summary['coeff of variation'] = params.cf_coeff
127+
if (params.cf_ploidy) summary['ploidy'] = params.cf_ploidy
128+
// }
129+
130+
// if ('haplotypecaller' in tools) summary['GVCF'] = params.no_gvcf ? 'No' : 'Yes'
131+
// if ('strelka' in tools && 'manta' in tools) summary['Strelka BP'] = params.no_strelka_bp ? 'No' : 'Yes'
132+
// if (params.pon && ('mutect2' in tools || (params.sentieon && 'tnscope' in tools))) summary['Panel of normals'] = params.pon
133+
134+
// if (params.annotate_tools) summary['Tools to annotate'] = annotate_tools.join(', ')
135+
136+
if (params.annotation_cache) {
137+
summary['Annotation cache'] = "Enabled"
138+
if (params.snpeff_cache) summary['snpEff cache'] = params.snpeff_cache
139+
if (params.vep_cache) summary['VEP cache'] = params.vep_cache
140+
}
141+
142+
if (params.cadd_cache) {
143+
summary['CADD cache'] = "Enabled"
144+
if (params.cadd_indels) summary['CADD indels'] = params.cadd_indels
145+
if (params.cadd_wg_snvs) summary['CADD wg snvs'] = params.cadd_wg_snvs
146+
}
147+
148+
if (params.genesplicer) summary['genesplicer'] = "Enabled"
149+
150+
if (params.igenomes_base && !params.igenomes_ignore) summary['AWS iGenomes base'] = params.igenomes_base
151+
if (params.igenomes_ignore) summary['AWS iGenomes'] = "Do not use"
152+
if (params.genomes_base && !params.igenomes_ignore) summary['Genomes base'] = params.genomes_base
153+
154+
summary['Save Reference'] = params.save_reference ? 'Yes' : 'No'
155+
156+
if (params.ac_loci) summary['Loci'] = params.ac_loci
157+
if (params.ac_loci_gc) summary['Loci GC'] = params.ac_loci_gc
158+
if (params.bwa) summary['BWA indexes'] = params.bwa
159+
if (params.chr_dir) summary['Chromosomes'] = params.chr_dir
160+
if (params.chr_length) summary['Chromosomes length'] = params.chr_length
161+
if (params.dbsnp) summary['dbsnp'] = params.dbsnp
162+
if (params.dbsnp_index) summary['dbsnp index'] = params.dbsnp_index
163+
if (params.dict) summary['dict'] = params.dict
164+
if (params.fasta) summary['fasta reference'] = params.fasta
165+
if (params.fasta_fai) summary['fasta index'] = params.fasta_fai
166+
if (params.germline_resource) summary['germline resource'] = params.germline_resource
167+
if (params.germline_resource_index) summary['germline resource index'] = params.germline_resource_index
168+
if (params.intervals) summary['intervals'] = params.intervals
169+
if (params.known_indels) summary['known indels'] = params.known_indels
170+
if (params.known_indels_index) summary['known indels index'] = params.known_indels_index
171+
if (params.mappability) summary['Mappability'] = params.mappability
172+
if (params.snpeff_cache) summary['snpEff cache'] = params.snpeff_cache
173+
if (params.snpeff_db) summary['snpEff DB'] = params.snpeff_db
174+
if (params.species) summary['snpEff species'] = params.species
175+
if (params.vep_cache) summary['VEP cache'] = params.vep_cache
176+
if (params.vep_cache_version) summary['VEP cache version'] = params.vep_cache_version
177+
90178
summary['Output dir'] = params.outdir
179+
summary['Publish dir mode'] = params.publish_dir_mode
180+
if (params.sequencing_center) summary['Sequenced by'] = params.sequencing_center
181+
91182
summary['Launch dir'] = workflow.launchDir
92183
summary['Working dir'] = workflow.workDir
93184
summary['Script dir'] = workflow.projectDir
94185
summary['User'] = workflow.userName
95-
if (workflow.profile.contains('awsbatch')) {
96-
summary['AWS Region'] = params.awsregion
97-
summary['AWS Queue'] = params.awsqueue
98-
summary['AWS CLI'] = params.awscli
99-
}
186+
187+
if (params.multiqc_config) summary['MultiQC config'] = params.multiqc_config
188+
100189
summary['Config Profile'] = workflow.profile
101-
if (params.config_profile_description) summary['Config Profile Descr'] = params.config_profile_description
102-
if (params.config_profile_contact) summary['Config Profile Contact'] = params.config_profile_contact
103-
if (params.config_profile_url) summary['Config Profile URL'] = params.config_profile_url
190+
191+
if (params.config_profile_description) summary['Description'] = params.config_profile_description
192+
if (params.config_profile_contact) summary['Contact'] = params.config_profile_contact
193+
if (params.config_profile_url) summary['URL'] = params.config_profile_url
194+
104195
summary['Config Files'] = workflow.configFiles.join(', ')
196+
105197
if (params.email || params.email_on_fail) {
106198
summary['E-mail Address'] = params.email
107199
summary['E-mail on failure'] = params.email_on_fail
108200
summary['MultiQC maxsize'] = params.max_multiqc_email_size
109201
}
202+
203+
if (workflow.profile.contains('awsbatch')) {
204+
summary['AWS Region'] = params.awsregion
205+
summary['AWS Queue'] = params.awsqueue
206+
summary['AWS CLI'] = params.awscli
207+
}
208+
110209
return summary
111210
}
112211

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