v1.0 Release Candidate #35
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Major rewrite
Template merge updates
maxulysse
reviewed
Nov 2, 2021
maxulysse
reviewed
Nov 2, 2021
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| samtools faidx $fasta | ||
| cut -f 1,2 ${fasta}.fai > ${fasta}.sizes | ||
| echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt |
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I think you can make it as a nf-core/modules, it's an easy command, but could be worth it to share with others
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Ok I will get this submitted
maxulysse
reviewed
Nov 2, 2021
maxulysse
reviewed
Nov 2, 2021
Fixed all dtypes for peak_repo script
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@maxulysse I cant see the unaddressed comments? thanks again for your review - I have resolved your comments. I will submit the get_chrom_sizes module, but if poss I would like to press ahead with release rather than waiting for that to be accepted into the modules repo. |
Readme changes
drpatelh
approved these changes
Nov 5, 2021
mashehu
reviewed
Nov 5, 2021
| @@ -0,0 +1,11 @@ | |||
| /* | |||
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I agree, you should untrack this file.
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| - [nf-core/cutandrun: Output](#nf-corecutandrun-output) | ||
| - [Introduction](#introduction) | ||
| - [Pipeline overview](#pipeline-overview) | ||
| - [Preprocessing](#preprocessing) | ||
| - [Samplesheet check](#samplesheet-check) | ||
| - [Fastq merging](#fastq-merging) | ||
| - [FastQC](#fastqc) | ||
| - [TrimGalore](#trimgalore) | ||
| - [Alignment](#alignment) | ||
| - [Bowtie 2](#bowtie-2) | ||
| - [Alignment post-processing](#alignment-post-processing) | ||
| - [samtools](#samtools) | ||
| - [picard MarkDuplicates/RemoveDuplicates](#picard-markduplicatesremoveduplicates) | ||
| - [Peak Calling](#peak-calling) | ||
| - [Bam to bedgraph](#bam-to-bedgraph) | ||
| - [Clip bedfiles](#clip-bedfiles) | ||
| - [Bed to bigwig](#bed-to-bigwig) | ||
| - [SEACR peak calling](#seacr-peak-calling) | ||
| - [BEDtools](#bedtools) | ||
| - [Reporting](#reporting) | ||
| - [Python reporting](#python-reporting) | ||
| - [MultiQC](#multiqc) | ||
| - [IGV](#igv) | ||
| - [Deeptools](#deeptools) | ||
| - [Workflow reporting and genomes](#workflow-reporting-and-genomes) | ||
| - [Reference genome files](#reference-genome-files) | ||
| - [Pipeline information](#pipeline-information) |
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No need for a markdown based ToC anymore. It will be generated from the headings on the website automatically
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