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base repository: quinlan-lab/STRling-nf
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base: v1.0.1
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head repository: quinlan-lab/STRling-nf
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compare: main
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  • 7 commits
  • 2 files changed
  • 2 contributors

Commits on Sep 9, 2021

  1. updates usage

    brwnj committed Sep 9, 2021
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  2. updates usage

    brwnj committed Sep 9, 2021
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Commits on Oct 15, 2021

  1. disable default reporting

    brwnj authored Oct 15, 2021

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Commits on Nov 4, 2021

  1. improves RAM allocations

    brwnj committed Nov 4, 2021
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Commits on Feb 8, 2022

  1. Update README.md

    fixing typo
    wdecoster authored Feb 8, 2022

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  2. Merge pull request #1 from wdecoster/patch-1

    Update README.md
    brwnj authored Feb 8, 2022

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Showing with 8 additions and 10 deletions.
  1. +5 −3 README.md
  2. +3 −7 nextflow.config
8 changes: 5 additions & 3 deletions README.md
Original file line number Diff line number Diff line change
@@ -3,17 +3,19 @@ A Nextflow implementation of the STRling data flow:
https://github.com/quinlan-lab/STRling

STRling: a method to detect novel (and reference) STR
expandsions from short-read data.
expansions from short-read data.

# Usage

To run joint calls across more than one sample on version 1.0 of the workflow:
To run joint calls across more than one sample on the `main` branch of the workflow:

```
nextflow run quinlan-lab/STRling-nf -r 1.0 \
nextflow run quinlan-lab/STRling-nf -r main -profile docker \
--joint --crams 'preprocessing/*.bam' --reference GRCh38.fasta \
```

Alternately, `-r` can designate tags, e.g. `-r v1.0.1`.

The workflow expects the alignments to be indexed (contain a .bai/.crai)
in the same directory as the .bam/.cram. It also expects the reference
.fasta to be indexed (.fai) and be in the same directory as the .fasta.
10 changes: 3 additions & 7 deletions nextflow.config
Original file line number Diff line number Diff line change
@@ -19,8 +19,8 @@ params {
}

process {
time = 4.h
memory = 8.GB
time = 24.h
memory = { 7.GB * task.attempt }
cpus = 1
container = 'brwnj/strling:v0.5.0'
cache = 'lenient'
@@ -29,8 +29,7 @@ process {
memory = 120.GB
}
withName: strling_call {
time = 24.h
memory = 24.GB
memory = { 4.GB * task.attempt }
}
}

@@ -48,15 +47,12 @@ profiles {
process.shell = ['/bin/bash', '-euo', 'pipefail']

timeline {
enabled = true
file = "${params.outdir}/logs/timeline.html"
}
report {
enabled = true
file = "${params.outdir}/logs/report.html"
}
trace {
enabled = true
file = "${params.outdir}/logs/trace.txt"
}