Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nf-core/modules issues and pull requests

#3826 - prepare_circ_test.R create duplication

Issue - State: open - Opened by yingfang3333 about 1 year ago
Labels: bug

#3825 - add kalign

Pull Request - State: closed - Opened by luisas about 1 year ago
Labels: Ready for Review

#3824 - Update stub and relevant tests for gatk's germlinecnvcaller

Pull Request - State: closed - Opened by ramprasadn about 1 year ago

#3823 - Picard modules: Include check input-ouput naming convention

Pull Request - State: closed - Opened by Joon-Klaps about 1 year ago - 1 comment

#3822 - Add a parameter corresponding to -canonList <file> option of snpEff ann

Issue - State: open - Opened by YeHW about 1 year ago - 4 comments
Labels: enhancement

#3821 - Add --annotate flag to CNVKIT_BATCH

Issue - State: open - Opened by SpikyClip about 1 year ago - 1 comment
Labels: enhancement

#3820 - update germlinecnvcaller

Pull Request - State: closed - Opened by ramprasadn about 1 year ago

#3819 - Picard modules disambiguate

Issue - State: closed - Opened by Joon-Klaps about 1 year ago
Labels: bug

#3817 - add module for btyper3

Pull Request - State: open - Opened by rpetit3 about 1 year ago
Labels: new module

#3816 - new module: Btyper3

Issue - State: open - Opened by rpetit3 about 1 year ago
Labels: new module

#3815 - fix empty channel assignment in FASTQ_TRIM_FASTP_FASTQC subworkflow

Pull Request - State: closed - Opened by Daniel-VM about 1 year ago - 2 comments

#3814 - new module: learnMSA/align

Issue - State: closed - Opened by luisas about 1 year ago
Labels: new module

#3813 - update GATK's annotateintervals and filterintervals, and CNVkit's batch with extra meta fields

Pull Request - State: closed - Opened by ramprasadn about 1 year ago - 2 comments
Labels: Ready for Review

#3812 - Update lofreq call & lofreq callparallel modules

Pull Request - State: closed - Opened by nevinwu about 1 year ago - 2 comments

#3811 - sentieon/dnascope : Handling args

Pull Request - State: closed - Opened by asp8200 about 1 year ago

#3810 - LOFREQ_CALL & LOFREQ_CALLPARALLEL modules should have an "intervals" input channel

Issue - State: closed - Opened by nevinwu about 1 year ago
Labels: enhancement, update module

#3809 - Add nf-test for fastq_trim_fastp_fastqc subworkflow

Pull Request - State: open - Opened by adamrtalbot about 1 year ago - 6 comments

#3808 - Move from paths-filter

Issue - State: open - Opened by Emiller88 about 1 year ago - 1 comment
Labels: bug

#3807 - Re-structure nf-test test files

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 2 comments

#3806 - bump wfmash to v0.10.5

Pull Request - State: closed - Opened by subwaystation about 1 year ago

#3805 - bump odgi modules to v0.8.3

Pull Request - State: closed - Opened by subwaystation about 1 year ago

#3804 - New module: quilt/quilt

Pull Request - State: closed - Opened by atrigila about 1 year ago - 2 comments
Labels: new module, ready to merge

#3803 - Update bamcmp

Pull Request - State: closed - Opened by SPPearce about 1 year ago

#3802 - Bamcmp sw

Pull Request - State: closed - Opened by SPPearce about 1 year ago - 1 comment

#3801 - Update SAMTOOLS_DEPTH

Pull Request - State: closed - Opened by nevinwu about 1 year ago

#3800 - Configure Renovate

Pull Request - State: closed - Opened by Emiller88 about 1 year ago

#3799 - Update a few container declarations

Issue - State: open - Opened by Emiller88 about 1 year ago
Labels: bug

#3798 - ci: Try setup-apptainer

Pull Request - State: closed - Opened by Emiller88 about 1 year ago - 9 comments

#3797 - Add Renovate

Issue - State: closed - Opened by Emiller88 about 1 year ago

#3796 - Fix output for bcl2fastq & bclconvert

Pull Request - State: closed - Opened by Aratz about 1 year ago - 6 comments

#3795 - ci: Switch to setup-nextflow

Pull Request - State: closed - Opened by Emiller88 about 1 year ago - 1 comment
Labels: tests

#3794 - `bcl2fastq` and `bclconvert` exclude some `.fastq.gz` files from the output

Issue - State: closed - Opened by Aratz about 1 year ago
Labels: bug

#3793 - Added support for multiple regions and added per-site r^2 optional output

Pull Request - State: closed - Opened by saulpierotti about 1 year ago - 1 comment

#3792 - RFC: New module exomiser-cli

Pull Request - State: open - Opened by matthdsm about 1 year ago

#3791 - update GTDB-tk to 2.3.2

Pull Request - State: closed - Opened by maxibor about 1 year ago

#3790 - Update sentieon dnascope

Pull Request - State: closed - Opened by asp8200 about 1 year ago

#3789 - Number of cpu is not adapted for fastp tool

Issue - State: open - Opened by mAGLAVE about 1 year ago

#3788 - Fix Pangolin Docker container name

Pull Request - State: closed - Opened by adalpino-illumina about 1 year ago - 1 comment

#3787 - Update amrfinderplus

Pull Request - State: closed - Opened by jasmezz about 1 year ago

#3786 - new module: CheckM2

Issue - State: open - Opened by willros about 1 year ago
Labels: new module

#3785 - Fix BCL Convert Container Name

Pull Request - State: closed - Opened by adalpino-illumina about 1 year ago - 6 comments

#3784 - Update bakta to v1.8.2

Pull Request - State: closed - Opened by jasmezz about 1 year ago

#3783 - new module: quilt

Issue - State: closed - Opened by atrigila about 1 year ago
Labels: new module

#3782 - Update taxpasta 0.5.0

Pull Request - State: closed - Opened by sofstam about 1 year ago

#3781 - Fix documentation link

Pull Request - State: open - Opened by pbiology over 1 year ago - 2 comments

#3780 - Fix filename check for cellranger count

Pull Request - State: closed - Opened by grst over 1 year ago

#3779 - qualimap/rnaseq: add meta information for references

Pull Request - State: closed - Opened by rannick over 1 year ago

#3778 - Update pointers to test data to static GitHub links

Issue - State: open - Opened by pinin4fjords over 1 year ago

#3777 - kallisto: add meta information for references

Pull Request - State: closed - Opened by rannick over 1 year ago
Labels: update module, Ready for Review

#3776 - Adding stubs to three Sentieon modules

Pull Request - State: closed - Opened by asp8200 over 1 year ago

#3775 - update smoothxg to v0.7.1

Pull Request - State: closed - Opened by subwaystation over 1 year ago

#3774 - fix bclconvert output glob

Pull Request - State: closed - Opened by matthdsm over 1 year ago

#3772 - New module: star/starsolo

Pull Request - State: closed - Opened by Joaodemeirelles over 1 year ago
Labels: new module

#3771 - STAR: update

Pull Request - State: closed - Opened by rannick over 1 year ago
Labels: update module, Ready for Review

#3770 - update arriba to 2.4.0 and add meta info to references

Pull Request - State: closed - Opened by rannick over 1 year ago

#3769 - new module: starsolo

Issue - State: closed - Opened by Joaodemeirelles over 1 year ago
Labels: new module

#3768 - update dumpsoftwareversions

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 2 comments

#3767 - update gfaffix to 0.1.5

Pull Request - State: closed - Opened by subwaystation over 1 year ago

#3766 - Stitch

Pull Request - State: closed - Opened by saulpierotti over 1 year ago - 6 comments
Labels: new module, Ready for Review

#3765 - New module: umitools/group

Pull Request - State: closed - Opened by Joon-Klaps over 1 year ago - 1 comment
Labels: new module, Ready for Review

#3764 - new module: umitools/group

Issue - State: closed - Opened by Joon-Klaps over 1 year ago
Labels: new module

#3763 - add new module for conifer

Pull Request - State: closed - Opened by icaromsc over 1 year ago - 1 comment
Labels: new module, ready to merge

#3762 - new module: conifer

Issue - State: closed - Opened by icaromsc over 1 year ago
Labels: new module

#3761 - Update test_data.config

Pull Request - State: closed - Opened by saulpierotti over 1 year ago - 3 comments

#3760 - Add sentieon tnscope

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 1 comment
Labels: Ready for Review

#3759 - new module: pasta/align

Issue - State: open - Opened by luisas over 1 year ago
Labels: new module

#3758 - Add sentieon tnscope

Pull Request - State: closed - Opened by ramprasadn over 1 year ago

#3757 - new module: kalign/align

Issue - State: closed - Opened by luisas over 1 year ago
Labels: new module

#3756 - new module: stitch

Issue - State: open - Opened by saulpierotti over 1 year ago
Labels: new module

#3755 - new module: staramr/search

Issue - State: open - Opened by apetkau over 1 year ago
Labels: new module

#3754 - Fix Snakemake output channel

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago

#3753 - Module quast update to meet guidelines again

Pull Request - State: closed - Opened by Joon-Klaps over 1 year ago
Labels: enhancement, Ready for Review

#3752 - Removed the unnecessary `-c` option - Modules starting with "a"

Pull Request - State: closed - Opened by muffato over 1 year ago - 1 comment

#3751 - add bedtools groupby

Pull Request - State: closed - Opened by mashehu over 1 year ago
Labels: Ready for Review

#3750 - Add filter_vep

Pull Request - State: closed - Opened by ramprasadn over 1 year ago

#3749 - new module: bedtools/groupby

Issue - State: closed - Opened by mashehu over 1 year ago
Labels: new module

#3748 - Fixed bug raised in issue #3747

Pull Request - State: closed - Opened by a4000 over 1 year ago

#3747 - Error in VSEARCH_CLUSTER when args3 == "--clusters"

Issue - State: closed - Opened by a4000 over 1 year ago
Labels: bug

#3746 - This MD5 differs between Conda and Singularity

Pull Request - State: closed - Opened by muffato over 1 year ago
Labels: tests

#3745 - Mafft version update

Pull Request - State: closed - Opened by muffato over 1 year ago - 1 comment
Labels: update module

#3744 - Update main.nf

Pull Request - State: open - Opened by VDaric over 1 year ago - 1 comment
Labels: ready to merge

#3743 - Mmseqs: Documentation fix #3739

Pull Request - State: closed - Opened by kenibrewer over 1 year ago

#3742 - FastK has got a -M option to control the memory usage

Pull Request - State: closed - Opened by muffato over 1 year ago - 1 comment

#3741 - [WIP] Use built in GHA temp dir for running tests

Pull Request - State: open - Opened by adamrtalbot over 1 year ago - 2 comments

#3739 - Documentation: mmseqs_createdb output channel listed as bam instead of db

Issue - State: closed - Opened by kenibrewer over 1 year ago
Labels: bug

#3738 - GHA use shared singularity cache

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago
Labels: Ready for Review

#3737 - new module: blat

Issue - State: open - Opened by d-jch over 1 year ago
Labels: new module

#3736 - Added blat module

Pull Request - State: closed - Opened by d-jch over 1 year ago - 8 comments
Labels: ready to merge

#3735 - samtools faidx second argument

Issue - State: closed - Opened by cmatKhan over 1 year ago - 2 comments
Labels: bug

#3734 - Add module: Clustalo align

Pull Request - State: closed - Opened by luisas over 1 year ago
Labels: new module, Ready for Review

#3733 - update sentieon recipes

Pull Request - State: closed - Opened by ramprasadn over 1 year ago

#3732 - METABAT2: reduced number of mv operations

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 3 comments

#3731 - new module: clustalo/align

Issue - State: closed - Opened by luisas over 1 year ago
Labels: new module

#3730 - Add module: Clustalo guidetree

Pull Request - State: closed - Opened by luisas over 1 year ago
Labels: new module, Ready for Review

#3729 - new module: clustalo/guidetree

Issue - State: closed - Opened by luisas over 1 year ago
Labels: new module

#3728 - fixup: Snakemake meta.yml was incorrect

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago

#3727 - Add sentieon wgsmetrics

Pull Request - State: closed - Opened by ramprasadn over 1 year ago