add qualimap

[lpantano]

It would be redundant with rseqc maybe but I think is much faster for some cases and we can give the option to use one or another.

Is ok if I work on adding qualimap for QC?

[apeltzer]

Sure, why not ?

[lpantano]

I feel quite stupid, but I tried to add it (and I have done successful pipelines before with nf) but for some reason, it is only doing qualimap for one sample, maybe somebody can help me?

I added the code here: https://github.com/lpantano/rnaseq/blob/dev/main.nf#L896

like the output says:

>nextflow run main.nf -profile test --aligner hisat2 --skip_rseq --skip_genebody_coverage
N E X T F L O W  ~  version 19.04.0
Launching `main.nf` [amazing_ptolemy] - revision: 7b66a56c5b
Run Name          : amazing_ptolemy
Reads             : data/*{1,2}.fastq.gz
Data Type         : Single-End
Strandedness      : None
Trimming          : 5'R1: 0 / 5'R2: 0 / 3'R1: 0 / 3'R2: 0
Aligner           : HISAT2
Fasta Ref         : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa
GTF Annotation    : https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf
Save prefs        : Ref Genome: No / Trimmed FastQ: No / Alignment intermediates: No
Max Resources     : 6 GB memory, 2 cpus, 2d time per job
Output dir        : ./results
Launch dir        : /net/storage001.ib.cluster/om2/user/lpantano/pipelines/dev/rnaseq
Working dir       : /net/storage001.ib.cluster/om2/user/lpantano/pipelines/dev/rnaseq/work
Script dir        : /net/storage001.ib.cluster/om2/user/lpantano/pipelines/dev/rnaseq
User              : lpantano
Config Profile    : test
Config Description: Minimal test dataset to check pipeline function
executor >  local (51)
[32/0456b5] process > get_software_versions [100%] 1 of 1 ✔
[c4/877894] process > makeHisatSplicesites  [100%] 1 of 1 ✔
[6e/52e9c2] process > makeBED12             [100%] 1 of 1 ✔
[8f/4745c5] process > output_documentation  [100%] 1 of 1 ✔
[0e/813c47] process > fastqc                [100%] 4 of 4 ✔
[77/e257cd] process > trim_galore           [100%] 4 of 4 ✔
[f3/e96f0b] process > makeHISATindex        [100%] 1 of 1 ✔
[6b/759aa8] process > hisat2Align           [100%] 4 of 4 ✔
[96/ff288c] process > hisat2_sortOutput     [100%] 4 of 4 ✔
[cc/da35a8] process > preseq                [100%] 4 of 4 ✔
[a5/3396e3] process > markDuplicates        [100%] 4 of 4 ✔
[db/830b64] process > bam_subsample         [100%] 2 of 2 ✔
[ce/c18036] process > rseqc                 [100%] 4 of 4 ✔
[be/03b686] process > qualimap              [100%] 1 of 1 ✔
[4a/0b3b18] process > stringtieFPKM         [100%] 4 of 4 ✔
[c1/243485] process > featureCounts         [100%] 4 of 4 ✔
[56/25a2f2] process > dupradar              [100%] 4 of 4 ✔
[63/909808] process > sample_correlation    [100%] 1 of 1 ✔
[74/d31239] process > merge_featureCounts   [100%] 1 of 1 ✔
[c3/1b7469] process > multiqc               [100%] 1 of 1 ✔
Completed at: 02-May-2019 17:13:25
Duration    : 4m 8s
CPU hours   : 0.1
Succeeded   : 51

[apeltzer]

Probably used a queue channel for e.g. the reference data

[lpantano]

lol, ok, got it.

[drpatelh]

Yep.

file gtf from gtf_qualimap.collect()

Should fix it.

[lpantano]

thanks. That was fun!

[lpantano]

Ok, all is working and I am going through the list to make the pull request, but I have a couple of questions:

• the test with docker will probably fail because it hasn't qualimap there, do I need to do something to update it?
• lint tells me to update some conda packages, should go ahead even if I didn't change those steps?

Thanks!

[apeltzer]

Ideally, a.) should resolve itself once we updated the environment.yml on the dev branch. You can also open a separate PR to update some conda packages (please not STAR, there is a comment in the environment why not) which you could use in a separate PR to include qualimap before you actually do the final PR including the code for qualimap.

That way, the tests will find qualimap properly to test everything when you do your "real" PR ;-)

Since adding just some recipes shouldn't break things, I think its fine to do a separate PR that just includes the environment.yml and CHANGELOG changes. Maybe something we should document as well.

[lpantano]

Oh! that is smart :) I’ll do that PR first!