TAD callers and compartement with more than one resolution

[Nico-FR]

Hi, I have launched the pipeline with 6 resolutions:

--res_compartments '800000,400000,200000,100000,50000' \
--tads_caller 'insulation,hicexplorer' \
--res_tads '200000,100000,50000,25000,10000,5000'

And the pipeline has lauched 6 jobs.

[be/c8092b] process > tads_hicexplorer (Bovin-365... [100%] 6 of 6 ✔
[22/7ac14e] process > tads_insulation (Bovin-3654... [100%] 6 of 6 ✔

However I have only one output:

ls ./tads/hicexplorer/
tad_boundaries.bed  tad_boundaries.gff  tad_domains.bed  tad_score.bedgraph

The same for insulation and compartement calling.

ls ./tads/insulation/
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_insulation.tsv

ls ./compartments
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_compartments.cis.E1.bedgraph
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_compartments.cis.lam.txt
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_compartments.cis.vecs.tsv

It seems that they are overwrite by each job because they all have the same prefix. Here is the command run by the pipeline for hicexplorer:

hicFindTADs --matrix Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_5000_norm.cool           
--outPrefix tad         
--correctForMultipleTesting fdr         
--numberOfProcessors 4

For more clarity I would recommend to keep the prefix of the input in full (I was wondering if it took normalized matrices or not).

hicFindTADs --matrix Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_5000_norm.cool           
--outPrefix Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_5000_norm         
--correctForMultipleTesting fdr         
--numberOfProcessors 4

[Nico-FR]

If it help, distance_decay works fine:

ls ./dist_decay/
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_10000_norm_distcount.png
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_10000_norm_distcount.txt
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_200000_norm_distcount.png
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_200000_norm_distcount.txt
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_50000_norm_distcount.png
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_50000_norm_distcount.txt
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_5000_norm_distcount.png
Bovin-3654_CCGCGGTT-CTAGCGCT-AHT2HCDSX2_L004_5000_norm_distcount.txt

[nservant]

fixed in the DSL2 version