Ecosyste.ms: Issues

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GitHub / cdcgov/mycosnp issues and pull requests

#21 - Update README.md

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

#20 - Max number of samples for pipeline

Issue - State: open - Opened by aharring83 over 2 years ago

#19 - Initial test of mycoSNP fails at checkpoint for step step.mask_repeats

Issue - State: open - Opened by jmrybak over 2 years ago - 2 comments

#18 - Formatting error for qc_report.txt

Issue - State: open - Opened by PHemarajata over 2 years ago - 1 comment

#17 - Workflow stuck at picard-markduplicates-gf2

Issue - State: closed - Opened by PHemarajata over 2 years ago

#16 - Release 0.22 changes. New run-mycosnp-single.sh wrapper script and up…

Pull Request - State: closed - Opened by mciprianoCDC almost 3 years ago - 1 comment

#15 - Working with Nextflow Workflows

Issue - State: closed - Opened by erinyoung about 3 years ago - 1 comment

#14 - Add instructions for updating workflows for state labs

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: documentation

#13 - Symbolic links to input files/folders not working

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: bug

#12 - Seqtk downsample step does not mount input directory properly

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment

#11 - Single VCF output

Issue - State: closed - Opened by jhphan over 3 years ago - 2 comments
Labels: enhancement

#10 - Broad VCF to FASTA python script not working as expected.

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: bug

#9 - Add comprehensive QC metrics

Issue - State: open - Opened by jhphan over 3 years ago
Labels: enhancement

#9 - Add comprehensive QC metrics

Issue - State: open - Opened by jhphan over 3 years ago
Labels: enhancement

#8 - BAM file not written for select samples

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: bug

#7 - Update to reference masking step to Mummer 4.0

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: enhancement

#6 - FaQCs output is empty

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: bug

#5 - Allow input of a single file that contains a list of multiple files/folders

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: enhancement

#4 - Hard to track workflow version numbers.

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: enhancement

#3 - Non-standard headers inside FASTQ files cause workflow to fail.

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: bug

#2 - Recognize unconventional naming convention for input files

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: enhancement

#1 - FAQCs Error with unequal R1 and R2 files

Issue - State: closed - Opened by jhphan over 3 years ago - 1 comment
Labels: bug