This PR adds a new subworkflow to immuno.cwl which creates summary tables in csv format containing information requested by the FDA for clinical cases. Several new tools are introduced, including FastQC, which was specifically requested by the FDA, as well as custom scripts for both unaligned and aligned data to calculate requested metrics not generated by FastQC or other existing upstream tools (eg, picard, flagstat). A host of new inputs are added to the immuno workflow to gather requested sequencing and sample information (eg, sequencing instrument, total amount of DNA/RNA).
This PR adds a new subworkflow to
immuno.cwlwhich creates summary tables in csv format containing information requested by the FDA for clinical cases. Several new tools are introduced, including FastQC, which was specifically requested by the FDA, as well as custom scripts for both unaligned and aligned data to calculate requested metrics not generated by FastQC or other existing upstream tools (eg, picard, flagstat). A host of new inputs are added to theimmunoworkflow to gather requested sequencing and sample information (eg, sequencing instrument, total amount of DNA/RNA).