The following snakemake code fails to produce multiqc output although it does for orther RSeQC tools including geneBody_coverage, junction_saturation, and read_distribution (removed here for clarity)
rule rseqc_cliping_profile:
"""
Run RSeQC on merged bam files
"""
input:
bam = "results/mappings/{smp}_mappings.bam"
output:
pdf3 = "results/rseqc2/{smp}.clipping_profile.R1.pdf",
pdf4 = "results/rseqc2/{smp}.clipping_profile.R2.pdf",
xls = "results/rseqc2/{smp}.clipping_profile.xls"
shell: """
mkdir -p intermediate/rseqc2
# Run clipping_profile.py
clipping_profile.py -i {input.bam} \
-q 30 \
-s PE \
-o intermediate/rseqc2/{wildcards.smp} \
&& cp -f intermediate/rseqc2/{wildcards.smp}.clipping_profile.R1.pdf {output.pdf3} \
&& cp -f intermediate/rseqc2/{wildcards.smp}.clipping_profile.R2.pdf {output.pdf4} \
&& cp -f intermediate/rseqc2/{wildcards.smp}.clipping_profile.xls {output.xls}
"""
Any idea about what I am doing wrong?
the results in intermediate/rseqc2 are of the kind (S12 only here):
S12.clipping_profile.r
S12.clipping_profile.R1.pdf
S12.clipping_profile.R2.pdf
S12.clipping_profile.xls
multiqc -f -i "RSeQC" -o intermediate/multiqc_rseqc2 -n multiqc_rseqc2 intermediate/rseqc2
[INFO ] multiqc : This is MultiQC v1.6
[INFO ] multiqc : Template : default
[INFO ] multiqc : Report title: RSeQC
[INFO ] multiqc : Searching 'intermediate/rseqc2'
[WARNING] multiqc : No analysis results found. Cleaning up..
[INFO ] multiqc : MultiQC complete
It is not a snakemake issue!
Although clipping_profile is in my multiqc config yaml, it seems not fit to find the clipping_profile data for plotting.
The xls file are in fact tsv files in disguise; renaming them .txt or .tsv does not improve the odds.
The MultiQC documentation on RSeQC support shows that MultiQC does not support that particular tool (clipping_profile), but it does support the others you mentioned.