Hi Jun, thanks a lot for your input which is extremely helpful.
On Sat, May 09, 2020 at 10:10:33PM +0200, Jun Aruga wrote: > Hi Andreas, > > The 3 pipelines nf-core/nanoseq, nf-core/artic, nf-core/viralrecon I > shared are the most applicable (= the highest priority) to COVID-19 > analysis. [1]. > Now I share the additional 5 pipelines that are certainly relevant (= > the 2nd highest priority). [2] > This is the result of my interview in the nf-core Slack channel. Thanks for doing this. > Could you check the packages situations in Debian? Done below. Every package without a remark is in Debian. I gave upstream URLs for those packages that are not yet touched and URLs on salsa.debian.org for preliminary packaging stuff. Sometimes I had some additional comments from previous experience. > Sorry I knew information about the 5 pipelines a few weeks ago. But I > took a time to summarize the list of the packages and email it. That's fine. We found other work to do meanwhile. ;-) > * nf-core/scrnaseq (single cell) > * nf-core/smartseq2 (single cell) > * nf-core/sarek (whole-genome sequencing) > * nf-core/mag (meta-genomics) > * nf-core/bcellmagic (immune response) > > https://github.com/nf-core/scrnaseq/blob/master/bin/scrape_software_versions.py > bustools -> https://bustools.github.io/ > kallisto > multiqc > salmon > star In Debian named rna-star > https://github.com/nf-core/smartseq2/blob/master/bin/scrape_software_versions.py > fastqc > multiqc > > https://github.com/nf-core/sarek/blob/master/bin/scrape_software_versions.py > allelecount -> https://github.com/cancerit/alleleCount > ascat -> https://github.com/Crick-CancerGenomics/ascat > bcftools > bwa > fastqc > freebayes > gatk -> https://salsa.debian.org/med-team/gatk > htslib > manta -> https://salsa.debian.org/med-team/manta May be somebody volunteers to ping upstream about a Python3 port here https://github.com/Illumina/manta/issues/180 We can not get it into Debian before this is solved. > multiqc > qualimap -> https://salsa.debian.org/med-team/qualimap I once was pretty close to package this. However it contains some binary JARs named bioinfo-commons-0.10.1.jar, bioinfo-ngs-0.1.0.jar, ... where the source just seems to be "lost". See my discussion on the mailing list: https://groups.google.com/forum/#!msg/qualimap/KVJ8m5ZsAhU/O30pHTkADAAJ;context-place=searchin/qualimap/org.bioinfo If anybody has some idea where to find those sources that would be really helpful! > r > samtools > snpeff -> https://salsa.debian.org/med-team/snpeff > strelka -> https://github.com/Illumina/strelka/ > tiddit -> https://github.com/SciLifeLab/TIDDIT > vcftools > vep Please confirm that you mean https://github.com/Ensembl/ensembl-vep > https://github.com/nf-core/mag/blob/master/bin/scrape_software_versions.py > busco -> https://gitlab.com/ezlab/busco > cat -> https://github.com/dutilh/CAT BTW, its not a good idea to name a tool like a pretty generid UNIX command > centrifuge > fastp > fastqc > filtlong > kraken2 > megahit -> https://ftp-master.debian.org/new/megahit_1.2.9-1.html (just uploaded to new) > metabat -> https://bitbucket.org/berkeleylab/metabat > multiqc > nanolyse -> https://pypi.org/project/NanoLyse/1.1.0/ (with version tag) -> Asked for release tags on https://github.com/wdecoster/nanolyse/issues/6 > nanoplot -> https://salsa.debian.org/med-team/nanoplot > porechop > quast -> https://salsa.debian.org/med-team/quast As I wrote in some other mail this itself has a lot of predepends that are included as binaries. > spades > > https://github.com/nf-core/bcellmagic/blob/master/bin/scrape_software_versions.py > changeo > fastqc > multiqc > muscle > presto Binary package name is python3-presto > r > r-alakazam Binary package name is r-cran-alakazam > r-shazam Binary package name is r-cran-shazam > r-tigger Binary package name is r-cran-tigger > vsearch If anybody wants to work on one of the packages its probably helpful to announce it here. Kind regards and thanks again for your very helpful contribution Andreas. > [1] nf-core Slack #covid19 channel > https://nfcore.slack.com/archives/C0105J0J9T8/p1587480925053900 > > The pipelines you listed are the ones that are/will be most > applicable to COVID-19 analysis. > [2] nf-core Slack #covid19 channel > https://nfcore.slack.com/archives/C0105J0J9T8/p1587498948095200 > > But the single cell pipelines could certainly be relevant. Also > sarek for whole-genome sequencing analysis, mag for metagenomics > analysis and bcellmagic for investigations into the immune response.. > > Thanks & Cheers, > Jun > > -- > Jun | He - His - Him > > -- http://fam-tille.de
