clockwork

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QC pipeline with script only

4

Hello, I want to update the new version, but I can not see how to QC when running only the script without tracking the database. I want to use this...

khoahoc0508

approach to classify mutations

5

Hello~ I have used clockwork to generate final.vcf files using the script only approach. Any advises or tools I can adopt to further analyze the final.vcf files? I would like...

alantsangmb

ERROR : Unknown image format/type

4

I am stuck trying to troubleshoot this error when I run 'clockwork' command. I downloaded the version clockwork_v0.11.3.img and have made it executable with chmod. I have singularity version 2.4.2-dist...

DOH-KEW4303

gnuplot error libQt5Core.so.5: cannot open shared object file: No such file or directory

1

Hi, I get this error midway through the QC pipeline: singularity exec clockwork_v0.11.2.img gnuplot work/db/92b468c299f88b7834a8461efb75b2/samtools_qc/samtools_qc.plot-quals.gp /usr/bin/gnuplot: error while loading shared libraries: libQt5Core.so.5: cannot open shared object file: No such file...

mehc555

Hi, I'm trying to remove contamination using the following commands: >$nextflow run ~/clockwork/nextflow/remove_contam.nf -with-singularity ~/clockwork/singularity/clockwork_container.img --ref_fasta ~/clockwork/ref_data/OUT/ref.fa --ref_metadata_tsv ~/clockwork/ref_data/OUT/remove_contam_metadata.tsv --reads_in1 1_1.fq --reads_in2 1_2.fq --outprefix remove_contam.out and got the error message:...

carolynzy

Hello, When I run `sudo singularity build clockwork.img clockwork_container.def` , throw error `2021/11/13 15:54:03 bufio.Scanner: token too long FATAL: Unable to build from clockwork_container.def: while parsing definition: clockwork_container.def: bufio.Scanner: token...

YuanDaoDao001

Zhicheng-Liu

Clobber (and warn about) existing output directories instead of bailing

2

Instead of failing an assertion when an output dir already exists this will replace it and log a warning. Prevents partial pipeline failures for resumed QC pipeline runs.

jeff-k

Count the number of positions with coverage above certain thresholds as part of QC. This should detect amplicon sequences.

jeff-k

Some stats we could add, requested in our WHO/UNITAID call 1. output a warning if any resistance gene has 5x depth 2. warn if 5x depth Summarise QC, Mykrobe, variant...

iqbal-lab