Multiqc medaka

[henningonsbring]

The purpose of the code changes are as follows:

• Adding multiqc for nanopore medaka workflow

Standard test procedure

• [ ] The self-test mentioned in the README finished successfully
• [ ] Produced files contain expected values
• [ ] The code has been reviewed by @octocat

This version is a:

• [ ] MAJOR - when you make incompatible API changes
• [ ] MINOR - when you add functionality in a backwards compatible manner
• [ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

[henningonsbring]

Now it is working, from base directory for the analysis (files contain the content they should contain):

ll QCStats/
total 64
drwxrws---+ 2 hiseq.clinical users 32768 Jul 25 15:21 articNcovNanopore_sequenceAnalysisMedaka_fastqcNanopore
drwxrws---+ 3 hiseq.clinical users  4096 Jul 25 15:22 articNcovNanopore_sequenceAnalysisMedaka_multiqcNanopore

ll QCStats/articNcovNanopore_sequenceAnalysisMedaka_fastqcNanopore/
total 62976
-rw-rw----+ 1 hiseq.clinical users 777909 Jul 25 15:21 01_SE100_22CS999701_1_fastqc.html
-rw-rw----+ 1 hiseq.clinical users 462712 Jul 25 15:21 01_SE100_22CS999701_1_fastqc.zip
-rw-rw----+ 1 hiseq.clinical users 671670 Jul 25 15:21 01_SE100_22CS999702_1_fastqc.html
-rw-rw----+ 1 hiseq.clinical users 424206 Jul 25 15:21 01_SE100_22CS999702_1_fastqc.zip
-rw-rw----+ 1 hiseq.clinical users 677384 Jul 25 15:21 01_SE100_22CS999703_1_fastqc.html
-rw-rw----+ 1 hiseq.clinical users 424779 Jul 25 15:21 01_SE100_22CS999703_1_fastqc.zip
-rw-rw----+ 1 hiseq.clinical users 703598 Jul 25 15:21 01_SE100_22CS999704_1_fastqc.html
-rw-rw----+ 1 hiseq.clinical users 430184 Jul 25 15:21 01_SE100_22CS999704_1_fastqc.zip
...

ll QCStats/articNcovNanopore_sequenceAnalysisMedaka_multiqcNanopore/
total 1792
drwxrws---+ 2 hiseq.clinical users    4096 Jul 25 15:22 noblecat_220725-151938_multiqc_data
-rw-rw----+ 1 hiseq.clinical users 1661333 Jul 25 15:22 noblecat_220725-151938_multiqc.html

[sofstam]

lgtm!

[JD2112]

@henningonsbring Nice! but need to add fastqc and multiqc in the Nanopore environment file. Could you please add that also to this PR?

[henningonsbring]

sure @JD2112, will fix

[henningonsbring]

Added and tested the container, is it ok to merge?

[JD2112]

Yes, sure. Thank you so much.