Code

[Feature Addition: Salmon]#221

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apeltzer merged 166 commits intodevnf-core/rnaseq:devfrom salmonnf-core/rnaseq:salmonCopy head branch name to clipboardJul 8, 2019

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Commits

Commits on May 29, 2019

• Addhtseq to environment requirements

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• Add HTSeq to changelog

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• small change to trigger build

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• Add v1.4dev section and move change there

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• Merge branch 'dev' into patch-1

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• Merge pull request #209 from olgabot/patch-1

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Commits on Jun 3, 2019

• Add salmon to requirements

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• Update changelog with salmon=0.14.0

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• Add salmon index

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• Add transcriptome to test config

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• fa --> fasta

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• Less character width to specify transcriptome in summary

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• Add salmon quant

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• add raw_salmon channel

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• Add salmon index to changelog

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• Add salmon to usage

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• Output salmon index to reference_transcriptome folder

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• write out more docs for salmon index

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• Add cpus for salmon quant

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• Add gtf for gene summarization

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Commits on Jun 4, 2019

• use BOTH salmon_quant and salmon_index configs

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• use same cpu, memory for both salmon quant and index

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• semicolon, not comma -_-;;;

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• Add merging of salmon gene and transcript counts

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• Don't need salmon quant twice

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• Add merging of transcript id to gene name mapping

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Commits on Jun 5, 2019

• Merge pull request #210 from czbiohub/olgabot/add-salmon

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• Move salmon to after featurecounts to use featurecounts output

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• Add scraping software versions

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• Separate transcript and gene count merging

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• Output sample name with trimmed reads

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• try some different logic to get salmon quant to run enough times

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• fix more salmon merging commands

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• try to get salmon quant to work on each file individually

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• Add changes from @kerimoff

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• force matplotlib to be 3.0.3

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• Update CHANGELOG.md

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• Get salmon merging to work

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• salmon_index --> makeSalmonIndex

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• Add escaped backslashes

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• add r-base 3.5.1 to speed up docker build

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• Update CHANGELOG.md

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• Merge pull request #214 from nf-core/lpantano-multiqc-patch-1

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Commits on Jun 6, 2019

• Add salmon to requirements

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• Update changelog with salmon=0.14.0

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• force matplotlib to be 3.0.3

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• Update CHANGELOG.md

  

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• add r-base 3.5.1 to speed up docker build

  

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• Update CHANGELOG.md

  

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• Make label for salmon to simplify cpu/memory config

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• Add salmon to multiqc

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Commits on Jun 7, 2019

• Merge pull request #212 from czbiohub/olgabot/salmon-quant

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• Adding in Lorena and Olga

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• Rephrased Changelog

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• Adjust the summary

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• Adding Salmon to MultiQC logs

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• Should have the salmon module now

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Commits on Jun 8, 2019

• Fix summary transcriptome statement

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• Use condition instead of duplicating code :)

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• Fix parentheses

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• MultiQC logging working now

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• Merge pull request #218 from apeltzer/salmon

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• Merge branch 'dev' into salmon

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Commits on Jun 9, 2019

• Update docs/output.md

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• Update main.nf

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• Update main.nf

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• Update main.nf

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• Update main.nf

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• Update main.nf

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• Update main.nf

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• Update main.nf

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• Mini change to add aligner to help

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• Adding transcriptome option to parameters.settings.json

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• Merge pull request #222 from apeltzer/salmon

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• Merge branch 'dev' into salmon

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Commits on Jun 10, 2019

• First pass update of relevant files

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• Fix lint errors and warnings

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• Reorder parameters

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• Rename Salmon processes

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• Use correct strandedness

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• Reorder validate inputs

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• Merge pull request #223 from drpatelh/salmon

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• Bug fixes

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• Merge pull request #224 from drpatelh/salmon

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Commits on Jun 11, 2019

• Add empty salmon_multiqc_logs channel

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Commits on Jun 12, 2019

• Fix merge conflicts

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Commits on Jun 13, 2019

• Major overhaul of Salmon requirements

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• Update CHANGELOG

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• Merge pull request #232 from drpatelh/salmon

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• Add tximport function

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• add docs for tximport

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• update readme and changelog

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• Merge pull request #233 from nf-core/lpantano-tximport

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Commits on Jun 15, 2019

• fix variable and correct version to parse gtf

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Commits on Jun 16, 2019

• Merge pull request #234 from nf-core/lpantano-salmon-patch

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Commits on Jun 18, 2019

• Close outstanding issues and amend salmon merge

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• Update CHANGELOG

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• Merge pull request #236 from drpatelh/salmon

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• Remove subsamp_filesize_thresh parameter

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• Merge pull request #237 from drpatelh/salmon

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Commits on Jun 21, 2019

• Don't extract transcripts if transcript_fasta is provided

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• Read transcript_fasta from config genome

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• fix typo in 'pseudo_aligner'

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• fix typo in object name

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• Fix logic for both star index provided + salmon for fasta

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• --transcriptome --> --transcript_fasta

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Commits on Jun 22, 2019

• Merge pull request #239 from pilm-bioinformatics/lpantano-salmon-tximport-patch

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Commits on Jun 23, 2019

• Merged my dev with upstream dev

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• Add in ReadGroups for QualiMap compatibility

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• Fix typo

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• Fix seqCenter

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• HISAT2 seq_center

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Commits on Jun 25, 2019

• Revert "Read transcript_fasta from config genome"

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• Change logic to deal with both salmon + alignment and fasta references

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• Add --gencode flag to salmon index'

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• --transcriptome --> --transcript_fasta

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• Only transfer quant.sf files for salon_merge"

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• Add separate step to clean featurecounts output to minimize memory needed for merging

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• Make salmon_merge also mid_memory

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• missing 'into'

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• Get clean_featureCounts to work with test data

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• Use all quant files into salmon_merge -- Reverts 44b7686

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• remove git cruft

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• fix mismatch between tx2gene and quant.sf

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• Use paste to merge everything

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Commits on Jun 26, 2019

• Use params.gencode to decide on --gencode flag

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• use evaluated $gencode parameter

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• add default value for gencode

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• Set params.fc_group_features_type = 'gene_type' if gencode

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• Add note about --gencode for usage"

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• Add note about --gencode for changelog

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Commits on Jun 27, 2019

• no "markdups" in filename

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• Update docs/usage.md

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• Use @drpatelh's description

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• Apply suggestions from code review

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• Remove reference to PR for changelog

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• evaluate params.fc_group_features_type within featureCounts process

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• Use unix-fu to merge featurecounts

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• Wrap biotype variable in braces

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• use 'bash' for syntax of fasta/gtf to fix markdownlint

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• Remove first line of featurecounts files

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• Evaluate gene biotype earlier and print in summary

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• Remove csvtk from requirements

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• add a note about redirection

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• Use @drpatelh's wording

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• remove random fenced code

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• Use 7th column for gene namec

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• Shorten name of biotype field in summary for brevity

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• use 0'th item not 1th

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• Add sample name to output

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• use tximport for each sample and then merge individually

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• properly merge gene counts and tpm files

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Commits on Jun 28, 2019

• actually use the gene counts to merge ..

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• Add transcript_id and gene_id to salmon output csv

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• Add --gencode flag to usage and summary output

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• Don't need salmon RDS files

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Commits on Jul 1, 2019

• Add gtf_qualimap

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Commits on Jul 2, 2019

• Merge pull request #242 from czbiohub/olgabot/salmon-gencode

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Commits on Jul 7, 2019

• Merge pull request #243 from czbiohub/olgabot/featurecounts-merge-memory

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• Merge pull request #244 from pilm-bioinformatics/lpantano-salmon-tximport-patch

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• Remove trailing slash

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• Merge branch 'dev' into salmon

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Commits on Jul 8, 2019

• Merge pull request #241 from apeltzer/salmon-readgroups

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• Merged

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• Merge branch 'dev' into salmon

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• Merged changes

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