update dev_rnaseq_vG brach to master #168
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…version Metagenomics Illumina Nextflow workflow
Changed text in "updates" section to more clearly explain the change in step 14d and fixed the capitalization on the GTDB-Tk software package.
…nversion Update description of changes
…version Metagenomics Nextflow workflow: Added post-processing workflow
…version Metagenomics Illumina Nextflow workflow: Edited README files and accession parameter
…Metagenomics_Illumina_NF_conversion
…version Nextflow Metagenomics Illumina conversion: Added missing post-processing script and fixed no assemblies produced bug
added dp_tools software to software table
Fixed treatment vector to always assign "treatment" state to 1st group in contrasts vector and "control" state to 2nd group.
Fixed treatment vector to always assign "treatment" state to 1st group in contrasts vector and "control" state to 2nd group.
* improved checkm performance by running separately on every bin * fixed typo in config * updated the nextflow version * changed the default value of accession input parameter * reverted AmpIllumina pipeline doc to remove updates * added launchDir variable * made format changes to config files * updated README * updated MGIllumina pipeline doc after CCB approval * added launch scripts and fixed bugs * deleted cluster path * fixed humman utilities mounting bug * commented out singularity cache_dir * updated the content of processing_info.zip to match other GeneLab Nextflow workflows
- Updated Pipeline doc
- added missing output files for assembly based processing
- added links between steps for file references
- fixed step references
- Created examples/runsheet folder for CSV examples files
- Added runsheet documentation
- Updated ChangeLog
- added ChangeLog documentation
- reformatted references to pipeline and previous snakemake workflow
- added closed issue references
- added other workflow specific updates vs previous snakemake
workflow (checkm implementation)
- Updated Workflow README
- add docker references since both Docker and Singularity are
supported
- regularize capitalization of Nextflow and Singularity to match
the tools' documentation
- reorganize post-processing output definition to match other assays
- clarify installation instructions for conda in workflow document
- Added missing assay suffix to "Failed" assembly file name
- Rename NF_MGIllumina-A to NF_MGIllumina
- Checked and updated all broken links
- Pipeline doc - fixed typo in sed command - NF workflow doc - added explicit definitions for all profiles available - removed slurm from example command-line calls - updated headings to adjust slurm removal - simplified instructions for different run approaches - added conda env configuration information as additional information under the conda profile definition.
…sion
Metagenomics Illumina NF conversion and pipeline update
Pipeline updates:
- Update tool versions
- FastQC
- MultiQC
- bowtie2
- samtools
- CAT
- GTDB-Tk
- HUMAnN
- MetaPhlAn
- In step 14d, MAG taxonomic classification, added the new --skip_ani_screen argument to gtdbtk classify_wf to continue classifying genomes as in previous versions of GTDB-Tk, using mash and skani.
Workflow updates:
- Update to the latest pipeline version (GL-DPPD-7101-A)
- Implement workflow in Nextflow (NF_MGIllumina) rather than Snakemake as in previous workflow versions.
- Run checkm separately on each bin and combine results to improve performance
Workflow Bug fixes:
- Allow explicit specification of the humann3 database location [Metagenomics Illumina] explicitly setting humann3 reference db locations in rule, fixes issue #62
- Package bin and MAGs fasta files into per sample zip archives [Metagenomics Illumina] Some datasets have too many files in the MAGs and bins folders, fixes issue #76
RNASeq Pipeline (7101-G and 7115) and workflow updates (NF_RCP v2.0.0)
- Fixed qc_metrics generation - Added qc_metrics documentation
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