Ecosyste.ms: Issues

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GitHub / stjudecloud/workflows issues and pull requests

#50 - fix: Remove read_string() outputs

Pull Request - State: closed - Opened by a-frantz over 3 years ago - 1 comment

#49 - fix(fastq_screen): catch and fast fail on intermittent bug

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#49 - fix(fastq_screen): catch and fast fail on intermittent bug

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#48 - docs: update README and workflow/tool headers

Pull Request - State: closed - Opened by a-frantz over 3 years ago - 5 comments

#48 - docs: update README and workflow/tool headers

Pull Request - State: closed - Opened by a-frantz over 3 years ago - 5 comments

#47 - fix(htseq): add arbitrarily large number to max-reads-in-buffer

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#47 - fix(htseq): add arbitrarily large number to max-reads-in-buffer

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#46 - PAPIv2 Key [disk] not supported by GCP backend

Issue - State: closed - Opened by TomGardner over 3 years ago - 5 comments

#46 - PAPIv2 Key [disk] not supported by GCP backend

Issue - State: closed - Opened by TomGardner over 3 years ago - 5 comments

#45 - workflows/rnaseq: 2.1.0 is not backward compatible with 2.0.0

Issue - State: closed - Opened by zaeleus over 3 years ago - 3 comments

#45 - workflows/rnaseq: 2.1.0 is not backward compatible with 2.0.0

Issue - State: closed - Opened by zaeleus over 3 years ago - 3 comments

#44 - Ngsderive multiqc

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#44 - Ngsderive multiqc

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#43 - Wdldoc refactor

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#43 - Wdldoc refactor

Pull Request - State: closed - Opened by a-frantz over 3 years ago

#42 - refactor: remove specifications that GTF must be from Gencode

Pull Request - State: closed - Opened by a-frantz almost 4 years ago - 1 comment

#42 - refactor: remove specifications that GTF must be from Gencode

Pull Request - State: closed - Opened by a-frantz almost 4 years ago - 1 comment

#41 - refactor(fastq_screen): remove need for specifically named DB

Pull Request - State: closed - Opened by a-frantz almost 4 years ago - 1 comment

#41 - refactor(fastq_screen): remove need for specifically named DB

Pull Request - State: closed - Opened by a-frantz almost 4 years ago - 1 comment

#40 - feat: add sequencErr to QC

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

#40 - feat: add sequencErr to QC

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

#39 - feat: Junction annotation

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#39 - feat: Junction annotation

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#38 - refactor: use samtools quickcheck to do initial validation

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#38 - refactor: use samtools quickcheck to do initial validation

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#37 - Add xenograft cleansing support for RNA-Seq V2

Pull Request - State: closed - Opened by adthrasher almost 4 years ago - 1 comment
Labels: enhancement

#37 - Add xenograft cleansing support for RNA-Seq V2

Pull Request - State: closed - Opened by adthrasher almost 4 years ago - 1 comment
Labels: enhancement

#36 - feat: add encoding ngsderive module

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#36 - feat: add encoding ngsderive module

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#35 - ESTIMATE

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#35 - ESTIMATE

Pull Request - State: closed - Opened by a-frantz almost 4 years ago

#34 - feat: add subsampling option

Pull Request - State: closed - Opened by a-frantz almost 4 years ago - 6 comments

#34 - feat: add subsampling option

Pull Request - State: closed - Opened by a-frantz almost 4 years ago - 6 comments

#33 - Adding bwa wdl tool and docker image

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

#33 - Adding bwa wdl tool and docker image

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

#32 - Adding workflow from Fastqs for RNA-Seq V2.

Pull Request - State: closed - Opened by adthrasher almost 4 years ago - 8 comments

#32 - Adding workflow from Fastqs for RNA-Seq V2.

Pull Request - State: closed - Opened by adthrasher almost 4 years ago - 8 comments

#31 - Qc refactor

Pull Request - State: closed - Opened by a-frantz about 4 years ago - 4 comments

#31 - Qc refactor

Pull Request - State: closed - Opened by a-frantz about 4 years ago - 4 comments

#30 - fix: changes for dxWDL compatibility

Pull Request - State: closed - Opened by a-frantz about 4 years ago - 1 comment

#30 - fix: changes for dxWDL compatibility

Pull Request - State: closed - Opened by a-frantz about 4 years ago - 1 comment

#29 - tools/htseq: Add override or fix htseq-count max-reads-in-buffer option

Issue - State: closed - Opened by zaeleus about 4 years ago - 3 comments

#29 - tools/htseq: Add override or fix htseq-count max-reads-in-buffer option

Issue - State: closed - Opened by zaeleus about 4 years ago - 3 comments

#28 - HTSeq output rename

Pull Request - State: closed - Opened by adthrasher about 4 years ago

#28 - HTSeq output rename

Pull Request - State: closed - Opened by adthrasher about 4 years ago

#27 - Expression updates

Pull Request - State: closed - Opened by adthrasher over 4 years ago

#27 - Expression updates

Pull Request - State: closed - Opened by adthrasher over 4 years ago

#26 - Gzip fastqs

Pull Request - State: closed - Opened by a-frantz over 4 years ago - 3 comments

#26 - Gzip fastqs

Pull Request - State: closed - Opened by a-frantz over 4 years ago - 3 comments

#25 - Only run FastQ Screen on WGS and WES

Pull Request - State: closed - Opened by a-frantz over 4 years ago

#25 - Only run FastQ Screen on WGS and WES

Pull Request - State: closed - Opened by a-frantz over 4 years ago

#24 - Replacing lsf.conf with known good version using ${} syntax.

Pull Request - State: closed - Opened by adthrasher over 4 years ago

#24 - Replacing lsf.conf with known good version using ${} syntax.

Pull Request - State: closed - Opened by adthrasher over 4 years ago

#23 - fix: changed samtools index threads option

Pull Request - State: closed - Opened by jsunny23 over 4 years ago - 2 comments

#23 - fix: changed samtools index threads option

Pull Request - State: closed - Opened by jsunny23 over 4 years ago - 2 comments

#21 - Tsne updates

Pull Request - State: closed - Opened by adthrasher over 4 years ago

#21 - Tsne updates

Pull Request - State: closed - Opened by adthrasher over 4 years ago

#19 - improvement: tar qualimap outputs

Pull Request - State: closed - Opened by claymcleod over 4 years ago - 3 comments

#19 - improvement: tar qualimap outputs

Pull Request - State: closed - Opened by claymcleod over 4 years ago - 3 comments

#18 - Overall Improvements to the workflows

Pull Request - State: closed - Opened by jsunny23 over 4 years ago - 3 comments

#18 - Overall Improvements to the workflows

Pull Request - State: closed - Opened by jsunny23 over 4 years ago - 3 comments

#17 - qc workflow

Pull Request - State: closed - Opened by a-frantz almost 5 years ago - 11 comments

#16 - Adthrasher/dnanexus changes

Pull Request - State: closed - Opened by adthrasher almost 5 years ago

#16 - Adthrasher/dnanexus changes

Pull Request - State: closed - Opened by adthrasher almost 5 years ago

#15 - NGSderive step assumes plain text

Issue - State: closed - Opened by adthrasher almost 5 years ago - 1 comment

#14 - ci: potential improvements to miniwdl check step

Pull Request - State: closed - Opened by claymcleod almost 5 years ago - 2 comments

#13 - feat: add import_syntax_check to Github Actions

Pull Request - State: closed - Opened by a-frantz almost 5 years ago - 1 comment

#12 - feat: add a `miniwdl check` Github Action

Pull Request - State: closed - Opened by a-frantz almost 5 years ago - 1 comment

#11 - Add memory arg to picard.validate_bam

Pull Request - State: closed - Opened by a-frantz almost 5 years ago - 1 comment

#10 - improve: infer strandedness for counts

Pull Request - State: closed - Opened by claymcleod almost 5 years ago - 1 comment

#9 - Sorting

Pull Request - State: closed - Opened by adthrasher almost 5 years ago - 1 comment

#8 - improvement: fix all `miniwdl check` suggestions

Pull Request - State: closed - Opened by claymcleod almost 5 years ago

#7 - Documentation

Pull Request - State: closed - Opened by adthrasher almost 5 years ago - 2 comments

#6 - docs: update README.md with new banner

Pull Request - State: closed - Opened by claymcleod almost 5 years ago

#5 - A little winter cleaning

Pull Request - State: closed - Opened by claymcleod about 5 years ago - 1 comment
Labels: enhancement

#4 - Add `zip` to Dockerfile

Pull Request - State: closed - Opened by claymcleod about 5 years ago

#3 - Removing Picard MarkDuplicates step

Pull Request - State: closed - Opened by adthrasher about 5 years ago - 1 comment

#2 - Remove duplicate marking

Issue - State: closed - Opened by adthrasher about 5 years ago - 1 comment

#1 - [WIP] STAR Workflow v2.0.0

Pull Request - State: closed - Opened by claymcleod over 5 years ago - 11 comments