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No need for BAI when using uBAM #928

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merged 5 commits into from
Apr 25, 2023
Merged

No need for BAI when using uBAM #928

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db3a925
no need for bai when starting from ubam
maxulysse Feb 1, 2023
846e05d
bai could be [] when ubam
maxulysse Feb 1, 2023
bc63194
update CHANGELOG
maxulysse Feb 1, 2023
9f6f8c9
Merge branch 'dev' into ubam
maxulysse Mar 17, 2023
c800559
Merge branch 'dev' into ubam
maxulysse Apr 25, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#898](https://github.com/nf-core/sarek/pull/898) - Sync `TEMPLATE` with `tools` `2.7.2`
- [#898](https://github.com/nf-core/sarek/pull/898) - Nextflow minimal version is now `22.10.1`
- [#909](https://github.com/nf-core/sarek/pull/909) - Cache test data on GHA
- [#928](https://github.com/nf-core/sarek/pull/928) - No need for BAI when starting from uBAM
- [#935](https://github.com/nf-core/sarek/pull/935) - Add params `build_only_index` to only build index
- [#936](https://github.com/nf-core/sarek/pull/936) - Add params `donwload_cache` to download annotation cache
- [#942](https://github.com/nf-core/sarek/pull/942) - Update `README.md`
Expand All @@ -43,6 +44,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#894](https://github.com/nf-core/sarek/pull/894) - Add description to `--cnvkit_reference`
- [#894](https://github.com/nf-core/sarek/pull/894) - Remove methods description TODO prompt
- [#927](https://github.com/nf-core/sarek/pull/927) - Fix tumor only variant calling issues with freebayes following [#896](https://github.com/nf-core/sarek/pull/896)
- [#928](https://github.com/nf-core/sarek/pull/928) - Fix [#700](https://github.com/nf-core/sarek/issues/700)
- [#929](https://github.com/nf-core/sarek/pull/929) - Fix somatic variant calling issues with msisensor following [#896](https://github.com/nf-core/sarek/pull/896)
- [#941](https://github.com/nf-core/sarek/pull/941) - Fix json validation for `tools`, `skip_tools` and `use_gatk_spark` [#892](https://github.com/nf-core/sarek/issues/892)
- [#954](https://github.com/nf-core/sarek/pull/954) - Fix missing annotation keys with snpeff and ensemblvep for `hg19`
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4 changes: 2 additions & 2 deletions workflows/sarek.nf
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Expand Up @@ -1222,12 +1222,12 @@ def extract_csv(csv_file) {

// start from BAM
} else if (row.lane && row.bam) {
if (!row.bai) {
if (params.step != 'mapping' && !row.bai) {
error("BAM index (bai) should be provided.")
}
meta.id = "${row.sample}-${row.lane}".toString()
def bam = file(row.bam, checkIfExists: true)
def bai = file(row.bai, checkIfExists: true)
def bai = row.bai ? file(row.bai, checkIfExists: true) : []
def CN = params.seq_center ? "CN:${params.seq_center}\\t" : ''
def read_group = "\"@RG\\tID:${row.sample}_${row.lane}\\t${CN}PU:${row.lane}\\tSM:${row.patient}_${row.sample}\\tLB:${row.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\""

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