Merge pull request #129 from MaxUlysse/FixSyncPR

Fix bugs due to merging TEMPLATE Sync PR

CHANGELOG.md

@@ -34,6 +34,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a
 - [#110](https://github.com/nf-core/sarek/pull/110) - Fix `snpEff` report issue cf [#106](https://github.com/nf-core/sarek/issues/106)
 - [#126](https://github.com/nf-core/sarek/pull/126) - Fix `iGenomes` paths
 - [#127](https://github.com/nf-core/sarek/pull/127), [#128](https://github.com/nf-core/sarek/pull/128) - Fix `ASCAT`
+- [#129](https://github.com/nf-core/sarek/pull/129)- Fix issue with Channel `channel ch_software_versions_yaml`
+- [#129](https://github.com/nf-core/sarek/pull/129)- Apply @drpatelh fix for `mardown_to_html.py` compatibility with Python 2
+- [#129](https://github.com/nf-core/sarek/pull/129)- Removed `Python` `3.7.3` from conda environment due to incompatibility
+- [#129](https://github.com/nf-core/sarek/pull/129)- Change ascii characters that were not supported from the `output.md` docs
 
 ### `Deprecated`
 

bin/markdown_to_html.py

@@ -4,9 +4,10 @@
 import markdown
 import os
 import sys
+import io
 
 def convert_markdown(in_fn):
-    input_md = open(in_fn, mode="r", encoding="utf-8").read()
+    input_md = io.open(in_fn, mode="r", encoding='utf-8').read()
     html = markdown.markdown(
         "[TOC]\n" + input_md,
         extensions = [

conf/base.config

@@ -48,7 +48,7 @@ process {
     memory = {params.max_memory}
   }
 
-  withName:get_software_versions {
+  withName:Get_software_versions {
     cache = false
   }
 

docs/output.md

@@ -119,7 +119,7 @@ For all samples:
 - `duplicateMarked_[SAMPLE].tsv` and `recalibrated_[SAMPLE].tsv`
   - TSV files to start Sarek from `recalibration` or `variantcalling` steps for a specific sample.
 
-> :warning: Only with [`--sentieon`](usage.md#--sentieon)
+> `/!\` Only with [`--sentieon`](usage.md#--sentieon)
 
 For all samples:
 **Output directory: `results/Preprocessing/TSV`**
@@ -242,9 +242,9 @@ Using [Strelka Best Practices](https://github.com/Illumina/strelka/blob/v2.9.x/d
 
 #### Sentieon DNAseq
 
-> :warning: Only with [`--sentieon`](usage.md#--sentieon)
+> `/!\` Only with [`--sentieon`](usage.md#--sentieon)
 
-[Sentieon DNAseq](https://www.sentieon.com/products/#dnaseq) implements the same mathematics used in the Broad Institute’s BWA-GATK HaplotypeCaller 3.3-4.1 Best Practices Workflow pipeline.
+[Sentieon DNAseq](https://www.sentieon.com/products/#dnaseq) implements the same mathematics used in the Broad Institute's BWA-GATK HaplotypeCaller 3.3-4.1 Best Practices Workflow pipeline.
 
 For further reading and documentation see the [Sentieon DNAseq user guide](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/).
 
@@ -256,7 +256,7 @@ For all samples:
 
 #### Sentieon DNAscope
 
-> :warning: Only with [`--sentieon`](usage.md#--sentieon)
+> `/!\` Only with [`--sentieon`](usage.md#--sentieon)
 
 [Sentieon DNAscope](https://www.sentieon.com/products) calls SNPs and small indels.
 
@@ -270,7 +270,7 @@ For all samples:
 
 #### Sentieon TNscope
 
-> :warning: Only with [`--sentieon`](usage.md#--sentieon)
+> `/!\` Only with [`--sentieon`](usage.md#--sentieon)
 
 [Sentieon TNscope](https://www.sentieon.com/products/#tnscope) calls SNPs and small indels on an Tumor/Normal pair.
 
@@ -339,7 +339,7 @@ For all samples:
 - `TIDDIT_[SAMPLE].signals.tab`
   - tab file describing coverage across the genome, binned per 50 bp
 - `TIDDIT_[SAMPLE].ploidy.tab`
-  - tab file describing the estimated ploïdy and coverage across each contig
+  - tab file describing the estimated ploidy and coverage across each contig
 - `TIDDIT_[SAMPLE].old.vcf`
   - VCF including the low qualiy calls
 - `TIDDIT_[SAMPLE].wig`
@@ -349,7 +349,7 @@ For all samples:
 
 #### Sentieon DNAscope SV
 
-> :warning: Only with [`--sentieon`](usage.md#--sentieon)
+> `/!\` Only with [`--sentieon`](usage.md#--sentieon)
 
 [Sentieon DNAscope](https://www.sentieon.com/products) can perform structural variant calling in addition to calling SNPs and small indels.
 

docs/usage.md

@@ -292,7 +292,7 @@ Use this to disable g.vcf from `HaplotypeCaller`.
 ### --skip_qc
 
 Use this to disable specific QC and Reporting tools.
-Available: `all`, `bamQC`, `BCFtools`, `FastQC`, `MultiQC`, `samtools`, `vcftools`, `versions`
+Available: `all`, `bamQC`, `BaseRecalibrator`, `BCFtools`, `Documentation`, `FastQC`, `MultiQC`, `samtools`, `vcftools`, `versions`
 Default: `None`
 
 ### --skipQC

environment.yml

@@ -6,7 +6,6 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - conda-forge::python=3.7.3
   - conda-forge::markdown=3.1.1
   - conda-forge::pymdown-extensions=6.0
   - conda-forge::pygments=2.5.2

main.nf

@@ -30,14 +30,14 @@ def helpMessage() {
     nextflow run nf-core/sarek --input sample.tsv -profile docker
 
     Mandatory arguments:
-      --input                [file] Path to input TSV file on mapping, recalibrate and variantcalling steps
-                                    Multiple TSV files can be specified with quotes
-                                    Works also with the path to a directory on mapping step with a single germline sample only
-                                    Alternatively, path to VCF input file on annotate step
-                                    Multiple VCF files can be specified with quotes
-      -profile                [str] Configuration profile to use
-                                    Can use multiple (comma separated)
-                                    Available: conda, docker, singularity, test and more
+      --input                  [file] Path to input TSV file on mapping, recalibrate and variantcalling steps
+                                      Multiple TSV files can be specified with quotes
+                                      Works also with the path to a directory on mapping step with a single germline sample only
+                                      Alternatively, path to VCF input file on annotate step
+                                      Multiple VCF files can be specified with quotes
+      -profile                  [str] Configuration profile to use
+                                      Can use multiple (comma separated)
+                                      Available: conda, docker, singularity, test and more
       --genome                  [str] Name of iGenomes reference
       --step                    [str] Specify starting step
                                       Available: Mapping, Recalibrate, VariantCalling, Annotate
@@ -57,7 +57,7 @@ def helpMessage() {
                                       snpEff, VEP, merge
                                       Default: None
       --skip_qc                 [str] Specify which QC tools to skip when running Sarek
-                                      Available: all, bamQC, BCFtools, FastQC, MultiQC, samtools, vcftools, versions
+                                      Available: all, bamQC, BaseRecalibrator, BCFtools, Documentation, FastQC, MultiQC, samtools, vcftools, versions
                                       Default: None
       --annotate_tools          [str] Specify from which tools Sarek will look for VCF files to annotate, only for step annotate
                                       Available: HaplotypeCaller, Manta, Mutect2, Strelka, TIDDIT
@@ -622,7 +622,7 @@ process Get_software_versions {
     """
 }
 
-yamlSoftwareVersion = yamlSoftwareVersion.dump(tag:'SOFTWARE VERSIONS')
+ch_software_versions_yaml = ch_software_versions_yaml.dump(tag:'SOFTWARE VERSIONS')
 
 /*
 ================================================================================
@@ -1399,6 +1399,8 @@ process GatherBQSRReports {
     """
 }
 
+if ('baserecalibrator' in skipQC) baseRecalibratorReport.close()
+
 recalTable = recalTable.dump(tag:'RECAL TABLE')
 
 (recalTableTSV, recalTableSampleTSV) = recalTableTSV.mix(recalTableTSVnoInt).into(2)
@@ -3309,6 +3311,8 @@ process Output_documentation {
     output:
         file "results_description.html"
 
+    when: !('documentation' in skipQC)
+
     script:
     """
     markdown_to_html.py $output_docs -o results_description.html
@@ -3346,8 +3350,6 @@ workflow.onComplete {
     email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
     email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
 
-    // TODO nf-core: If not using MultiQC, strip out this code (including params.max_multiqc_email_size)
-    // On success try attach the multiqc report
     def mqc_report = null
     try {
         if (workflow.success) {
@@ -3541,7 +3543,9 @@ def defineAnnoList() {
 def defineSkipQClist() {
     return [
         'bamqc',
+        'baserecalibrator',
         'bcftools',
+        'documentation',
         'fastqc',
         'markduplicates',
         'multiqc',