Code polishing + add BWAMEM2_MEM process

[maxulysse]

╰─≻nextflow run . -profile docker,test_trimming -resume                                                                            
N E X T F L O W  ~  version 20.04.1
Launching `./main.nf` [naughty_jang] - revision: a5e99310b5
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
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            ___     __   __   __   ___     /,-._.--~'
      |\ | |__  __ /  ` /  \ |__) |__         }  {
      | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                            `._,._,'
          ____
        .´ _  `.
       /  |\`-_ \      __        __   ___     
      |   | \  `-|    |__`  /\  |__) |__  |__/
       \ |   \  /     .__| /¯¯\ |  \ |___ |  \
        `|____\´

      nf-core/sarek v3.0dev
----------------------------------------------------
Run Name            : naughty_jang
Input               : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv
Fasta File          : https://raw.githubusercontent.com/nf-core/test-datasets/sarek/reference/human_g1k_v37_decoy.small.fasta
Max Resources       : 6 GB memory, 2 cpus, 2d time per job
Container           : docker - nfcore/sarek:dev
Output dir          : ./results
Launch dir          : /home/maxime/workspace/nf-core_sarek
Working dir         : /home/maxime/workspace/nf-core_sarek/work
Script dir          : /home/maxime/workspace/nf-core_sarek
User                : maxime
Config Profile      : docker,test_trimming
Config Profile Descr: Minimal test dataset to check pipeline function
Config Files        : /home/maxime/.nextflow/config, /home/maxime/workspace/nf-core_sarek/nextflow.config
------------------------------------------------------
WARN: There's no process matching config selector: CONCATVCF
WARN: There's no process matching config selector: SNPEFF
executor >  local (2)
[ad/33a0d6] process > BUILD_INDICES:BWAMEM2_INDEX (human_g1k_v37_decoy.small.fasta)                                                [100%] 1 of 1, cached: 1 ✔
[af/4acc85] process > BUILD_INDICES:GATK_CREATE_SEQUENCE_DICTIONARY (human_g1k_v37_decoy.small.fasta)                              [100%] 1 of 1, cached: 1 ✔
[5c/36a7fc] process > BUILD_INDICES:SAMTOOLS_FAIDX (human_g1k_v37_decoy.small.fasta)                                               [100%] 1 of 1, cached: 1 ✔
[d4/90264e] process > BUILD_INDICES:HTSLIB_TABIX_DBSNP (dbsnp_138.b37.small.vcf.gz)                                                [100%] 1 of 1, cached: 1 ✔
[e9/bae9ef] process > BUILD_INDICES:HTSLIB_TABIX_KNOWN_INDELS (Mills_1000G_gold_standard_and_1000G_phase1.indels.b37.small.vcf.gz) [100%] 1 of 1, cached: 1 ✔
[01/f4a5e4] process > CREATE_INTERVALS_BED (small.intervals)                                                                       [100%] 1 of 1, cached: 1 ✔
[7c/85995d] process > FASTQC (1234-9876T_M5)                                                                                       [100%] 11 of 11, cached: 11 ✔
[36/a29edd] process > TRIM_GALORE (1234-9876T_M5)                                                                                  [100%] 11 of 11, cached: 11 ✔
[34/4f1d76] process > BWAMEM2_MEM (9876T_9876T_M5)                                                                                 [100%] 11 of 11, cached: 11 ✔
[57/f2b824] process > OUTPUT_DOCUMENTATION                                                                                         [100%] 1 of 1, cached: 1 ✔
[10/07685c] process > GET_SOFTWARE_VERSIONS                                                                                        [100%] 1 of 1 ✔
[36/6373ad] process > MULTIQC (1)                                                                                                  [100%] 1 of 1 ✔
-[nf-core/sarek] Pipeline completed successfully-
WARN: [nf-core/sarek] Could not attach MultiQC report to summary email

[maxulysse]

Finally decided to stick with Nextflow 20.04.1, but I think we need to try out 20.06.0-edge tomorrow.

[maxulysse]

• Sorry for going overboard and snake_case plenty of variables/functions.
• Decided to get rid of the ch_ prefix, not sure it's useful any more in the DSL2 context.
• did some code polishing
• improve and added BWAMEM2_MEM in our main workflow

I'm quite happy about:

sarek/modules/subworkflows/build_indices.nf

Lines 12 to 17 in 510a585

	include {
	HTSLIB_TABIX as HTSLIB_TABIX_DBSNP;
	HTSLIB_TABIX as HTSLIB_TABIX_GERMLINE_RESOURCE;
	HTSLIB_TABIX as HTSLIB_TABIX_KNOWN_INDELS;
	HTSLIB_TABIX as HTSLIB_TABIX_PON;
	} from '../nf-core/htslib_tabix'

and

sarek/modules/subworkflows/build_indices.nf

Lines 52 to 54 in 510a585

	if (!(params.intervals) && !('annotate' in step) && !('controlfreec' in step)) {
	BUILD_INTERVALS(SAMTOOLS_FAIDX.out)
	}