Updated flows, configs, and versions

• Added new role for nf-core pipelines and deleted separate roles for rnaseq, methylseq, ampliseq and atacseq
• Updated versions/configs for
  • nextflow
  • rnaseq
  • methylseq
  • multiqc
  • sarek - pulls config with nf-core and images from docker separately
  • neutronstar - updated version and added supernova
  • ngi_reports - removed xml generation
  • TACA - added TACA runfolder delivery
  • taca-ngi-pipeline - added xml generation to softstaging
  • statusdb
  • flowcell parser
• Removed link to standalone scripts for Uppsala.
• Update seqreports and piper paths for Uppsala deliveries.
• Fixed click version to v7.0 as v7.1 seems to break pipelines.

version updates

• Added atacseq and ampliseq
• removed nougat
• bumped reports, multiqc, taca, taca_ngi_pipeline
• Update ampliseq release version
• update arteria-delivery version
• update sispyhus version
• update ngi_pipeline version
• Bump multiqc_ngi version
• Changed methylseq config
• Restructured methylseq comments, not sure about comment syntax
• Format .config files with Nextflow syntax highlighting on GitHub
• sarek hooks in irma_ngi_config so that ngi_pipeline can launch sarek … …
• deploy Uppsala standalone scripts into the project directory as well
• Updated ngi-pipeline to fix yaml.load warning
• Methylseq qualimap bugfix just made things worse
• Update sthlm database url

Updated configs and versions of software

Updated versions of many tools as well as fixing Sarek configs.

Changelog:

• Bump methylseq, neutronstar, ngi reports, taca_ngi_pipeline, ngi_pipeline, Sarek, arteria-delivery, Nextflow, MultiQC_NGI, sisyphus
• deploy irma-specific sarek config
• Set MultiQC config.swedac_accredited according to NGI node
• removed delete parameter from rsync command
• Added memory specs for non-node jobs for sarek config

version updates etc.

This version includes some bugfixes, e.g.

• Removed NXF_WORK definition from Irma bashrc

Some tool versions were updated:

• update ngi_pipeline version
• Updating MultiQC and nf-core deployments
• bumped sarek version, stored nextflow url and version in a parameter
• updated neutronstar version

Some additional fixes:

• added standalone scripts for uppsala
• some clarification on deployments in README

New archive-upload version, methylation-related fixes, cleaned out sarek images

In this release:

• a methylseq alias was fixed and a temp/cache folder was added
• the archive-upload service previously had a problem with old errors causing trouble on new upload runs. This is fixed by using a new logfile every time archive-upload runs dsmc
• deprecated and no longer required docker containers were removed from the sarek installation

New archive-upload service, kong config etc.

With this release, a new version of snpseq-archive-upload is deployed (v1.0.0). Sarek has been updated to v2.2.0 and a fix for broken logging in ngi_pipeline has been addressed.

In addition, the kong config format has been changed.

The NGI workflow now explicitly states which versions of FastQC, FastQC_screen and bowtie are to be used.

A crontab entry was added to update charon for sarek jobs.

New archive-upload service, kong config etc.

With this release, a new version of snpseq-archive-upload is deployed (v1.0.0). Sarek has been updated to v2.2.0 and a fix for broken logging in ngi_pipeline has been addressed.

In addition, the kong config format has been changed.

New archive-upload service, kong config etc.

With this release, a new version of snpseq-archive-upload is deployed (v1.0.0). In addition, the kong config format has been changed.

Version updates for programs

This release mostly contains version updates for various tools

• ngi_report
• ngi_pipeline
• sarek
• taca_ngi_deliveries
• nf-core/methylseq (v1.1)
• nf-core/rnaseq (v1.0)
• MultiQC (v1.6)
• MultiQC_NGI (v0.6)

SAREK with other updates

This release includes the following changes

• sarek - CAW is now changed to sarek, the core functionality is pretty much the same but with cool new upgrades. More info can be found here

• MultiQC - is now upgraded to new release v1.5. More info on the release can found here

• NGI-RNASeq - is now upgraded to new release 1.4. More info on the release can be found here

• NGI-NeutronStar - a new package to handle chromium denovo project using supernova. Package description is found here

• Nougat - small package change and use of more singularity images

• Nextflow - use latest version available as the java issue is now handled

• taca-ngi-pipleine - couple of updates on how deliveries are done via taca