Change --sample by --input

CHANGELOG.md

@@ -43,17 +43,17 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#21](https://github.com/nf-core/sarek/pull/21) - Add tests for latest Nextflow version as well
 - [#21](https://github.com/nf-core/sarek/pull/21) - Add `genomes.config` for genomes without AWS iGenomes
 - [#24](https://github.com/nf-core/sarek/pull/24) - Added GATK4 Mutect2 calling and filtering
-- [#XXX](https://github.com/nf-core/sarek/pull/XXX) - Use Github actions for CI
+- [#27](https://github.com/nf-core/sarek/pull/27), [#30](https://github.com/nf-core/sarek/pull/30) - Use Github actions for CI, linting and branch protection
 - [#31](https://github.com/nf-core/sarek/pull/31) - Add nf-core lint
 - [#31](https://github.com/nf-core/sarek/pull/31) - Add extra CI to GitHub Actions nf-core extra CI
 
 ### `Changed`
 
-- [#1](https://github.com/nf-core/sarek/pull/1), [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#6](https://github.com/nf-core/sarek/pull/6), [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9), [#10](https://github.com/nf-core/sarek/pull/10), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12), [#18](https://github.com/nf-core/sarek/pull/18), [#20](https://github.com/nf-core/sarek/pull/20), [#21](https://github.com/nf-core/sarek/pull/21), [#29](https://github.com/nf-core/sarek/pull/29) - Update docs
+- [#1](https://github.com/nf-core/sarek/pull/1), [#2](https://github.com/nf-core/sarek/pull/2), [#3](https://github.com/nf-core/sarek/pull/3), [#4](https://github.com/nf-core/sarek/pull/4), [#5](https://github.com/nf-core/sarek/pull/5), [#6](https://github.com/nf-core/sarek/pull/6), [#7](https://github.com/nf-core/sarek/pull/7), [#8](https://github.com/nf-core/sarek/pull/8), [#9](https://github.com/nf-core/sarek/pull/9), [#10](https://github.com/nf-core/sarek/pull/10), [#11](https://github.com/nf-core/sarek/pull/11), [#12](https://github.com/nf-core/sarek/pull/12), [#18](https://github.com/nf-core/sarek/pull/18), [#20](https://github.com/nf-core/sarek/pull/20), [#21](https://github.com/nf-core/sarek/pull/21), [#23](https://github.com/nf-core/sarek/pull/23), [#29](https://github.com/nf-core/sarek/pull/29) - Update docs
 - [#4](https://github.com/nf-core/sarek/pull/4) - Update `cancerit-allelecount` from `2.1.2` to `4.0.2`
 - [#4](https://github.com/nf-core/sarek/pull/4) - Update `gatk4` from `4.1.1.0` to `4.1.2.0`
-- [#7](https://github.com/nf-core/sarek/pull/7) - `--sampleDir` is now deprecated, use `--sample` instead
-- [#7](https://github.com/nf-core/sarek/pull/8) - `--annotateVCF` is now deprecated, use `--sample` instead
+- [#7](https://github.com/nf-core/sarek/pull/7), [#23](https://github.com/nf-core/sarek/pull/23) - `--sampleDir` is now deprecated, use `--input` instead
+- [#7](https://github.com/nf-core/sarek/pull/8), [#23](https://github.com/nf-core/sarek/pull/23) - `--annotateVCF` is now deprecated, use `--input` instead
 - [#8](https://github.com/nf-core/sarek/pull/8), [#12](https://github.com/nf-core/sarek/pull/12) - Improve helper script `build.nf` for downloading and building reference files
 - [#9](https://github.com/nf-core/sarek/pull/9) - ApplyBQSR is now parallelized
 - [#9](https://github.com/nf-core/sarek/pull/9) - Fastq files are named following "${idRun}_R1.fastq.gz" in the FastQC output for easier reporting
@@ -73,7 +73,13 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#18](https://github.com/nf-core/sarek/pull/18), [#29](https://github.com/nf-core/sarek/pull/29) - `--noReports` is now `--skipQC all`
 - [#18](https://github.com/nf-core/sarek/pull/18), [#21](https://github.com/nf-core/sarek/pull/21) - Update logo
 - [#21](https://github.com/nf-core/sarek/pull/21) - Moved smallGRCh37 path to `genomes.config`
+- [#23](https://github.com/nf-core/sarek/pull/23) - Rename `genomeFile`, `genomeIndex` and  `genomeDict` by `fasta`, `fastaFai` and `dict`
+- [#23](https://github.com/nf-core/sarek/pull/23) - `--sample` is now deprecated, use `--input` instead
+- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeFile` is now deprecated, use `--fasta` instead
+- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeIndex` is now deprecated, use `--fastaFai` instead
+- [#23](https://github.com/nf-core/sarek/pull/23) - `--genomeDict` is now deprecated, use `--dict` instead
 - [#24](https://github.com/nf-core/sarek/pull/24) - iGenomes config now contains germline resource for GATK4 Mutect2
+- [#30](https://github.com/nf-core/sarek/pull/30) - Simplify code for `MapReads` process
 - [#31](https://github.com/nf-core/sarek/pull/31) - Move extra CI to GitHub Actions nf-core extra CI
 - [#32](https://github.com/nf-core/sarek/pull/32), [#33](https://github.com/nf-core/sarek/pull/33) - Install `ASCAT` with `conda` in the `environment.yml` file
 - [#33](https://github.com/nf-core/sarek/pull/33) - use workflow.manifest.version to specify workflow version in path to R scripts for control-FREEC and VEP processes
@@ -91,15 +97,16 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 ### `Fixed`
 
 - [#3](https://github.com/nf-core/sarek/pull/3) - Fix Docker ownership
-- [#11](https://github.com/nf-core/sarek/pull/11) - Fix MergeMpileup PublishDir
+- [#11](https://github.com/nf-core/sarek/pull/11) - Fix `MergeMpileup` PublishDir
 - [#13](https://github.com/nf-core/sarek/pull/13) - Fix merge in annotation
 - [#14](https://github.com/nf-core/sarek/pull/14) - Fix output name for vcf files
 - [#16](https://github.com/nf-core/sarek/pull/16) - Fix path to Rscript
 - [#18](https://github.com/nf-core/sarek/pull/18) - Improve cpu usage
 - [#18](https://github.com/nf-core/sarek/pull/18) - Use same font for nf-core and sarek in ascii art
 - [#20](https://github.com/nf-core/sarek/pull/20) - Use new logo in README
 - [#20](https://github.com/nf-core/sarek/pull/20) - Fix path to references genomes
-- [#22](https://github.com/nf-core/sarek/pull/22) - Fix --singleCPUMem issue
+- [#22](https://github.com/nf-core/sarek/pull/22) - Fix `--singleCPUMem` issue
+- [#30](https://github.com/nf-core/sarek/pull/30) - fix choice between `inputPairReadsFastQC` and `inputBAMFastQC` channels
 - [#31](https://github.com/nf-core/sarek/pull/31) - Fix badges according to nf-core lint
 - [#31](https://github.com/nf-core/sarek/pull/31) - Fix rcolorbrewer version according to nf-core lint
 - [#33](https://github.com/nf-core/sarek/pull/33) - Fix MD Linting

build.nf

@@ -186,9 +186,6 @@ process DecompressFile {
 ch_decompressedFiles = ch_decompressedFiles.dump(tag:'DecompressedFile')
 
 ch_fastaFile = Channel.create()
-ch_fastaForBWA = Channel.create()
-ch_fastaReference = Channel.create()
-ch_fastaForSAMTools = Channel.create()
 ch_otherFile = Channel.create()
 ch_vcfFile = Channel.create()
 

conf/genomes.config

@@ -15,9 +15,9 @@ params {
       bwaIndex         = "${params.genomes_base}/human_g1k_v37_decoy.fasta.{amb,ann,bwt,pac,sa}"
       dbsnp            = "${params.genomes_base}/dbsnp_138.b37.vcf"
       dbsnpIndex       = "${params.genomes_base}/dbsnp_138.b37.vcf.idx"
-      genomeDict       = "${params.genomes_base}/human_g1k_v37_decoy.dict"
-      genomeFile       = "${params.genomes_base}/human_g1k_v37_decoy.fasta"
-      genomeIndex      = "${params.genomes_base}/human_g1k_v37_decoy.fasta.fai"
+      dict             = "${params.genomes_base}/human_g1k_v37_decoy.dict"
+      fasta            = "${params.genomes_base}/human_g1k_v37_decoy.fasta"
+      fastaFai         = "${params.genomes_base}/human_g1k_v37_decoy.fasta.fai"
       intervals        = "${params.genomes_base}/wgs_calling_regions_Sarek.list"
       knownIndels      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
       knownIndelsIndex = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
@@ -32,9 +32,9 @@ params {
       dbsnpIndex            = "${params.genomes_base}/dbsnp_146.hg38.vcf.gz.tbi"
       germlineResource      = "${params.genomes_base}/GCF_000001405.38.AUTOSOMESXY.COMMON.BIALLELIC.SNPs.with.AF.vcf.gz"
       germlineResourceIndex = "${params.genomes_base}/GCF_000001405.38.AUTOSOMESXY.COMMON.BIALLELIC.SNPs.with.AF.vcf.gz.tbi"
-      genomeDict            = "${params.genomes_base}/Homo_sapiens_assembly38.dict"
-      genomeFile            = "${params.genomes_base}/Homo_sapiens_assembly38.fasta"
-      genomeIndex           = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.fai"
+      dict                  = "${params.genomes_base}/Homo_sapiens_assembly38.dict"
+      fasta                 = "${params.genomes_base}/Homo_sapiens_assembly38.fasta"
+      fastaFai              = "${params.genomes_base}/Homo_sapiens_assembly38.fasta.fai"
       intervals             = "${params.genomes_base}/wgs_calling_regions.hg38.bed"
       knownIndels           = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
       knownIndelsIndex      = "${params.genomes_base}/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"
@@ -49,9 +49,9 @@ params {
       dbsnpIndex            = "${params.genomes_base}/dbsnp_138.b37.small.vcf.idx"
       germlineResource      = "${params.genomes_base}/dbsnp_138.b37.small.vcf"
       germlineResourceIndex = "${params.genomes_base}/dbsnp_138.b37.small.vcf.idx"
-      genomeDict            = "${params.genomes_base}/human_g1k_v37_decoy.small.dict"
-      genomeFile            = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
-      genomeIndex           = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta.fai"
+      dict                  = "${params.genomes_base}/human_g1k_v37_decoy.small.dict"
+      fasta                 = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta"
+      fastaFai              = "${params.genomes_base}/human_g1k_v37_decoy.small.fasta.fai"
       intervals             = "${params.genomes_base}/small.intervals"
       knownIndels           = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf"
       knownIndelsIndex      = "${params.genomes_base}/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.small.vcf.idx"

conf/igenomes.config

@@ -17,9 +17,9 @@
        dbsnpIndex             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/dbsnp_138.b37.vcf.idx"
        germlineResource       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz"
        germlineResourceIndex  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh37.PASS.AC.AF.only.vcf.gz.tbi"
-       genomeDict             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
-       genomeFile             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
-       genomeIndex            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
+       dict                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.dict"
+       fasta                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta"
+       fastaFai               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.fai"
        intervals              = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/intervals/wgs_calling_regions_Sarek.list"
        knownIndels            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf"
        knownIndelsIndex       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/{1000G_phase1,Mills_and_1000G_gold_standard}.indels.b37.vcf.idx"
@@ -34,9 +34,9 @@
        dbsnpIndex             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi"
        germlineResource       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz"
        germlineResourceIndex  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GermlineResource/gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz.tbi"
-       genomeDict             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
-       genomeFile             = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
-       genomeIndex            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
+       dict                   = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict"
+       fasta                  = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta"
+       fastaFai               = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai"
        intervals              = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions.hg38.bed"
        knownIndels            = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz"
        knownIndelsIndex       = "${params.igenomes_base}/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi"

conf/test.config

@@ -15,7 +15,7 @@ params {
   max_memory = 6.GB
   max_time = 48.h
   // Input data
-  sample = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/tsv/tiny-manta-https.tsv'
+  input = 'https://github.com/nf-core/test-datasets/raw/sarek/testdata/tsv/tiny-manta-https.tsv'
   // Small reference genome
   // To be build with: `nextflow run build.nf --build -profile docker --outdir references`
   igenomesIgnore = true

docs/input.md

@@ -2,7 +2,7 @@
 
 ## Information about the TSV files
 
-Input files for Sarek can be specified using a TSV file given to the `--sample` command.
+Input files for Sarek can be specified using a TSV file given to the `--input` command.
 The TSV file is a Tab Separated Value file with columns:
 
 - `subject gender status sample lane fastq1 fastq2` for step `mapping` with paired-end FASTQs
@@ -49,10 +49,10 @@ G15511    XX    1    D0ENMT    D0ENM_2    pathToFiles/D0ENMACXX111207.2_1.fastq.
 
 ## Path to a FASTQ directory for a single normal sample (step mapping)
 
-Input files for Sarek can be specified using the path to a FASTQ directory given to the `--sample` command only with the `mapping` step.
+Input files for Sarek can be specified using the path to a FASTQ directory given to the `--input` command only with the `mapping` step.
 
 ```bash
-nextflow run nf-core/sarek --sample pathToDirectory ...
+nextflow run nf-core/sarek --input pathToDirectory ...
 ```
 
 ### Input FASTQ file name best practices
@@ -128,9 +128,9 @@ G15511    XX    1    D0ENMT    pathToFiles/G15511.D0ENMT.md.recal.bam    pathToF
 
 ## VCF files for annotation
 
-Input files for Sarek can be specified using the path to a VCF directory given to the `--sample` command only with the `annotate` step.
+Input files for Sarek can be specified using the path to a VCF directory given to the `--input` command only with the `annotate` step.
 Multiple VCF files can be specified if the path is enclosed in quotes.
 
 ```bash
-nextflow run nf-core/sarek --step annotate --sample "results/VariantCalling/*/.vcf.gz" ...
+nextflow run nf-core/sarek --step annotate --input "results/VariantCalling/*/.vcf.gz" ...
 ```