Ecosyste.ms: Issues

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

GitHub / nf-core/rnasplice issues and pull requests

#97 - Add some more tags to make the pipeline easier to find

Issue - State: open - Opened by FriederikeHanssen 11 months ago
Labels: enhancement

#96 - add zenodo doi

Pull Request - State: closed - Opened by maxulysse 12 months ago - 2 comments

#95 - bump version

Pull Request - State: open - Opened by jma1991 12 months ago - 1 comment

#94 - pre-release fixes

Pull Request - State: closed - Opened by jma1991 12 months ago - 1 comment

#93 - example contrastsheet.csv missing

Issue - State: closed - Opened by Kevin2197 12 months ago - 1 comment
Labels: bug

#92 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 1 comment

#91 - Potential fix for MISO index issue

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 1 comment

#90 - test profile: miso_index failure

Issue - State: closed - Opened by heathfuqua about 1 year ago - 19 comments
Labels: bug

#89 - MISO_SASHIMI error: Could not find MISO output files

Issue - State: closed - Opened by amizeranschi about 1 year ago - 4 comments
Labels: bug

#88 - refactor rmats contrasts

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 1 comment

#87 - replace across with combine to mimic SQL join

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 1 comment

#86 - suppa fix attempt 1

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 1 comment

#83 - STAGER error: subscript out of bounds

Issue - State: closed - Opened by paolo-kunderfranco about 1 year ago - 5 comments
Labels: bug

#82 - keep contrasts as array when only one level

Pull Request - State: closed - Opened by jma1991 about 1 year ago

#81 - EDGER_EXON fails if only single entry in contrast sheet

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

#80 - Fixes MISO scratch/launch directory and gffread issue

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 4 comments

#79 - Merging template updates

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 1 comment

#78 - The default --miso_genes are invalid when --gencode is specified and cause the pipeline to fail

Issue - State: closed - Opened by amizeranschi about 1 year ago - 2 comments
Labels: bug

#77 - V1.0.0 release fixes

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 1 comment

#76 - second pass of v1 fixes

Pull Request - State: closed - Opened by jma1991 about 1 year ago - 1 comment

#75 - MISO_SASHIMI looks in NXF_HOME subdirectory instead of working directory for output files

Issue - State: closed - Opened by dkoppstein about 1 year ago - 4 comments
Labels: bug

#74 - MISO_SASHIMI step fails when using scratch directory

Issue - State: closed - Opened by dkoppstein about 1 year ago - 2 comments
Labels: bug

#73 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago

#72 - GTF_2_GFF3 fails with latest Gencode GTF for human

Issue - State: closed - Opened by amizeranschi over 1 year ago - 21 comments
Labels: bug

#71 - SUPPA cluster events error

Issue - State: closed - Opened by paolo-kunderfranco over 1 year ago - 14 comments
Labels: bug

#70 - ERROR ~ No such variable: Exception evaluating property 'out' for nextflow.script.ChannelOut

Issue - State: closed - Opened by amizeranschi over 1 year ago - 7 comments
Labels: bug

#69 - DRIMSEQ_FILTER error

Issue - State: closed - Opened by paolo-kunderfranco over 1 year ago - 10 comments
Labels: bug

#68 - initial pass of fixes

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#67 - resolve gencode fix

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#66 - Revert "Fixed gencode issues"

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#65 - Fixed gencode issues

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

#64 - remove sniffer

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#62 - Revert "Fixed params.gencode in prepare_genome - issue #60"

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#61 - Fixed params.gencode in prepare_genome - issue #60

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

#60 - prepare_genome gencode

Issue - State: closed - Opened by tijeco over 1 year ago - 2 comments

#59 - prettier CHANGELOG

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#58 - Prettier CHANGELOG.md

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#57 - 1.0.0 release of nf-core/rnasplice pipeline

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 4 comments

#56 - release steps

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#55 - fix lint tests v1

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#54 - Merging template updates

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#53 - v1 of contrasts

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 2 comments

#52 - Implement pairwise DEXSeq contrasts

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#51 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago

#50 - Bam and visualisation

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#49 - update process capacity

Pull Request - State: closed - Opened by jma1991 over 1 year ago

#48 - Test full

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#47 - remove default values specified as None

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#46 - add basic tower.yml file

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#45 - update singularity and docker containers

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#44 - dexseq: stager.R: subscript out of bounds.

Issue - State: closed - Opened by gl9797 over 1 year ago - 2 comments
Labels: bug

#43 - fixed some pipeline and module tests

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#42 - Fix module tests

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 2 comments

#41 - fix duplicate exons and star segfault

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 2 comments

#40 - fix samplesheet location

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 2 comments

#39 - Fix full test sample sheet location

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 1 comment

#38 - remove enable_conda param

Pull Request - State: closed - Opened by jma1991 over 1 year ago - 2 comments

#37 - Merging template updates

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

#36 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago

#35 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#34 - SL-18 Update SAMTOOLS_INDEX publishDir pattern

Pull Request - State: closed - Opened by claire-prince almost 2 years ago - 1 comment

#33 - Sl 15 implement featurecounts for dex seq deu

Pull Request - State: closed - Opened by claire-prince almost 2 years ago - 1 comment

#32 - SL-21 Include enable.conda in configuration

Pull Request - State: closed - Opened by claire-prince almost 2 years ago - 1 comment

#31 - SL-13 Add param to turn off DEXSeq.gff output save

Pull Request - State: closed - Opened by claire-prince almost 2 years ago - 3 comments

#30 - SL-17 Include star_salmon_quant rule in modules.config

Pull Request - State: closed - Opened by claire-prince almost 2 years ago - 1 comment

#29 - Use script with echo + sed instead of exec with task.WorkDir for rMATS create_bamlist

Pull Request - State: closed - Opened by olgabot almost 2 years ago - 4 comments

#28 - Sl 64 write GitHub documentation

Pull Request - State: closed - Opened by bensouthgate almost 2 years ago - 1 comment

#27 - SL-117 fix featurecounts spec

Pull Request - State: closed - Opened by ghost almost 2 years ago - 1 comment

#26 - SL-119 add gtf_gene_filter to modules.config

Pull Request - State: closed - Opened by ghost almost 2 years ago - 1 comment

#25 - SL-118 respec modules conf

Pull Request - State: closed - Opened by ghost almost 2 years ago

#24 - SL-98 rmats read length correction

Pull Request - State: closed - Opened by asmaali98 almost 2 years ago - 1 comment

#23 - SL-104 fix withname pattern

Pull Request - State: closed - Opened by ghost almost 2 years ago

#22 - SL-112 add warning for user

Pull Request - State: closed - Opened by ghost almost 2 years ago - 1 comment

#21 - SL-106 check denominator specified correctly

Pull Request - State: closed - Opened by ghost almost 2 years ago

#20 - Sl 64 write GitHub documentation

Pull Request - State: closed - Opened by bensouthgate almost 2 years ago - 1 comment

#19 - SL-108 add single prep to withname pattern

Pull Request - State: closed - Opened by ghost almost 2 years ago

#18 - SL-105 add getchromsizes to modules conf

Pull Request - State: closed - Opened by ghost almost 2 years ago

#17 - SL-107 typo correction in dex seq

Pull Request - State: closed - Opened by asmaali98 almost 2 years ago - 1 comment

#16 - SL-99 add biocparallel

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#15 - SL-98 add rmats mulled container, resolve dexseq bug

Pull Request - State: closed - Opened by asmaali98 almost 2 years ago - 1 comment

#14 - SL-101 add suppa parameter check

Pull Request - State: closed - Opened by ghost almost 2 years ago - 1 comment

#13 - Sl 102 add condition check for rmats to groovy script

Pull Request - State: closed - Opened by ghost almost 2 years ago - 1 comment

#12 - Sl 96 refactor aligner conditional behaviour

Pull Request - State: closed - Opened by ghost almost 2 years ago

#11 - SL-95 format bin python files

Pull Request - State: closed - Opened by ghost almost 2 years ago - 1 comment

#10 - SL-93 refactor rmarts input checks

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#9 - SL-86 refactor ch_samplesheet

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#8 - SL-84 parametize gff type / add process_single tag

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#7 - SL-82 add groovy functions and include valid_params

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#6 - SL-70 Add strandedness,condition and validation code

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#5 - SL-78 update nf-core module structure imports

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#4 - SL-77 Add .github files

Pull Request - State: closed - Opened by ghost almost 2 years ago - 2 comments

#3 - SL-33 implement edge deu module

Pull Request - State: closed - Opened by ghost almost 2 years ago

#2 - Sl 35 rmats single condition

Pull Request - State: closed - Opened by bensouthgate almost 2 years ago

#1 - Sl 29 implement featurecount module

Pull Request - State: closed - Opened by ghost almost 2 years ago