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Change --sample by --input (#23)
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* feat: remove unnecessary Channel.create()
* feat: replace --sample with --input, genomeFile with fasta...
* feat: update comments
* feat: update docs
* add deprecation message for --sample, --sampleDir, --anotateVCF, --noReports, --genomeDict, --genomeFile, --genomeIndex
    - Add message when deprecated params are used
    - Deprecated params are still working
    - Fix usage of deprecated params
* Fix --input for germline sample directory
* tsvPath is now defined as null by default
* add deprecation info in docs about --noReports
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@maxulysse
maxulysse authored Sep 10, 2019
1 parent c0c08ae commit 5ea919f
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19 changes: 13 additions & 6 deletions CHANGELOG.md
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Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
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3 changes: 0 additions & 3 deletions build.nf
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Expand Up @@ -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()

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18 changes: 9 additions & 9 deletions conf/genomes.config
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Expand Up @@ -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"
Expand All @@ -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"
Expand All @@ -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"
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12 changes: 6 additions & 6 deletions conf/igenomes.config
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Expand Up @@ -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"
Expand All @@ -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"
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2 changes: 1 addition & 1 deletion conf/test.config
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Expand Up @@ -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
Expand Down
10 changes: 5 additions & 5 deletions docs/input.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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" ...
```
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