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Remove constitutive k-mers#131

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olgabot wants to merge 45 commits intodevnf-core/kmermaid:devfrom olgabot/remove-ribo-kmersnf-core/kmermaid:olgabot/remove-ribo-kmersCopy head branch name to clipboard

+649-230

Commits

Commits on Mar 9, 2021

• Remove SortMeRNA from requirements

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  7b147ba

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• Add Luiz's remove-many code

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  b3d415c

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• Remove SortMeRNA

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• Add parameters for housekeeping gene removal

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Commits on Mar 10, 2021

• Add mini refseq download option for testing

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• Add raw quote strings around nf-core lint

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  f27b037

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• Get fasta filtering working

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  c1e9c59

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• Update test params for download refseq

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• Add Rsync, return gxx linux

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• Add osx environment yml

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  caf4450

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• download refseq and filter fasta is working

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  5a56dde

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• Merge remote-tracking branch 'origin' into olgabot/remove-ribo-kmers

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• Add missing quote

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• Move merged sigs to view

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• Merge remote-tracking branch 'origin' into olgabot/remove-ribo-kmers

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• Add test_download_refseq to ci.yml

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  c5a0aae

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• Update scrape_software_versions

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• Remove sortmerna from get_software_versions

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  ba243e3

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• Fix sketch params in test_download_refseq

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• Got subtract to work!!

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Commits on Mar 11, 2021

• Use mamba to install packages

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• Move Rust to conda-forge section

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• Set sketch_scaled to 10 by default

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• reference_proteome_fasta --> translate_proteome_fasta

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• Use my branch of the rust sourmash remove code

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• Add cmake to help with gcc building

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  94d5f2c

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• Get housekeeping removal from sig, fasta to work

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  c7d603d

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• Update vital gene tests

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• Soft link conda C libraries

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Commits on Mar 12, 2021

• housekeeping --> constitutive

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Commits on Mar 15, 2021

• Add explicit path for conda bin

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• Actually do soft links

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• Update whitespace to make dockerfile more readable

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  8d73e30

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• Add separate creation of ch_refseq_moltypes_to_download

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  b4e91b8

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• Update tests to all use mini refseq data

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• Pipeline is running!

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• Get "sourmash compare" to run

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• Update constitutive rna sig for all configs

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Commits on Mar 16, 2021

• Add test_bam alone

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  dbf97f9

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• Update constitutive signatures

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• housekeeping --> constitutive

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• Reference proteome fasta --> translate_proteome_fasta

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• Move bam to input section

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• reference proteome fasta to translate_proteome_fasta in test_constitutive_from_fasta

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• Don't fail fast for all tests to see which individual ones are failing

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