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convoluted if statements to allow skipping
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@ktmeaton
ktmeaton committed May 8, 2020
1 parent 91c168d commit 6d8c592
Showing 1 changed file with 103 additions and 97 deletions.
200 changes: 103 additions & 97 deletions pipeline.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -287,7 +287,7 @@ if( (params.sqlite || ( params.ncbimeta_update && params.ncbimeta_annot) ) && !p

//-----------------------------Download Assembly Fasta------------------------//

if (!params.skip_assembly_download){
if (!params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process assembly_download{
/*
Expand Down Expand Up @@ -388,7 +388,7 @@ if (!params.skip_reference_download){
}
// -----------------------------Detect Repeats--------------------------------//

if (!params.skip_reference_detect_repeats){
if (!params.skip_reference_detect_repeats && !params.skip_reference_download){

process reference_detect_repeats{
/*
Expand Down Expand Up @@ -446,7 +446,7 @@ if (!params.skip_reference_detect_repeats){
}
// -------------------------Detect Low Complexity-----------------------------//

if (!params.skip_reference_detect_low_complexity){
if (!params.skip_reference_detect_low_complexity && !params.skip_reference_download){

process reference_detect_low_complexity{
/*
Expand Down Expand Up @@ -491,7 +491,7 @@ if (!params.skip_reference_detect_low_complexity){

// --------------------------------Pairwise Alignment-------------------------//

if(!params.skip_snippy_pairwise){
if(!params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process snippy_pairwise{
/*
Expand Down Expand Up @@ -570,7 +570,7 @@ if(!params.skip_snippy_pairwise){

// ------------------------Multi Sample Variant Summary-----------------------//

if(!params.skip_snippy_variant_summary){
if(!params.skip_snippy_variant_summary && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process snippy_variant_summary_collect{
/*
Expand Down Expand Up @@ -609,7 +609,7 @@ if(!params.skip_snippy_variant_summary){
}
// --------------------------Detect High SNP Density--------------------------//

if(!params.skip_snippy_detect_snp_high_density){
if(!params.skip_snippy_detect_snp_high_density && !params.skip_snippy_variant_summary && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process snippy_detect_snp_high_density{
/*
Expand Down Expand Up @@ -676,56 +676,57 @@ if(!params.skip_snippy_detect_snp_high_density){
}

// --------------------------Merge Filtering BED Files------------------------//
if(!params.skip_snippy_merge_mask_bed && !params.skip_snippy_variant_summary && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process snippy_merge_mask_bed{
/*
Combine, merge, and sort all BED file regions for masking the multiple alignment.
Input:
ch_bed_ref_detect_repeats (bed): A bed file containing regions of in-exact repeats from process reference_detect_repeats.
ch_bed_ref_low_complex (bed): A bed file containing regions of low-complexity regions from process reference_detect_low_complexity.
ch_snippy_subs_bed_density_multi (bed): Sorted and merged high density SNP regions from process snippy_sort_snp_high_density.
ch_bed_mask_master_merge (bed): Combined BED files of repeats, low-complexity and (optional) high-density SNP regions.
process snippy_merge_mask_bed{
/*
Combine, merge, and sort all BED file regions for masking the multiple alignment.
Output:
ch_bed_mask_snippy_multi (bed): Master masking BED file for process snippy_multi.
Input:
ch_bed_ref_detect_repeats (bed): A bed file containing regions of in-exact repeats from process reference_detect_repeats.
ch_bed_ref_low_complex (bed): A bed file containing regions of low-complexity regions from process reference_detect_low_complexity.
ch_snippy_subs_bed_density_multi (bed): Sorted and merged high density SNP regions from process snippy_sort_snp_high_density.
ch_bed_mask_master_merge (bed): Combined BED files of repeats, low-complexity and (optional) high-density SNP regions.
Publish:
master.bed (bed): Master masking BED file.
*/
// Other variables and config
tag "bed_snippy_subs_density"
publishDir "${outdir}/snippy_filtering", mode: 'copy'
if (params.skip_snippy_detect_snp_high_density){
ch_bed_ref_detect_repeats
.mix(ch_bed_ref_low_complex)
.collectFile(name: "master_unmerged_skip_snp_density.bed")
.set{ch_bed_mask_master_merge}
}
Output:
ch_bed_mask_snippy_multi (bed): Master masking BED file for process snippy_multi.
else{
Publish:
master.bed (bed): Master masking BED file.
*/
// Other variables and config
tag "bed_snippy_subs_density"
publishDir "${outdir}/snippy_filtering", mode: 'copy'
if (params.skip_snippy_detect_snp_high_density){
ch_bed_ref_detect_repeats
.mix(ch_bed_ref_low_complex, ch_snippy_subs_bed_density_multi)
.collectFile(name: "master_unmerged.bed")
.mix(ch_bed_ref_low_complex)
.collectFile(name: "master_unmerged_skip_snp_density.bed")
.set{ch_bed_mask_master_merge}
}
// IO and conditional behavior
input:
file bed_mask from ch_bed_mask_master_merge
output:
file "master.bed" into ch_bed_mask_snippy_multi
}

// Shell script to execute
script:
"""
cat ${bed_mask} | sort -k1,1 -k2,2n | bedtools merge > master.bed
"""
}
else{
ch_bed_ref_detect_repeats
.mix(ch_bed_ref_low_complex, ch_snippy_subs_bed_density_multi)
.collectFile(name: "master_unmerged.bed")
.set{ch_bed_mask_master_merge}
}
// IO and conditional behavior
input:
file bed_mask from ch_bed_mask_master_merge
output:
file "master.bed" into ch_bed_mask_snippy_multi

// Shell script to execute
script:
"""
cat ${bed_mask} | sort -k1,1 -k2,2n | bedtools merge > master.bed
"""
}
}

//------------------------------Multiple Alignment----------------------------//

if(!params.skip_snippy_multi){
if(!params.skip_snippy_multi && !params.skip_snippy_merge_mask_bed && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process snippy_multi{
/*
Expand Down Expand Up @@ -776,7 +777,7 @@ if(!params.skip_snippy_multi){

}

if(!params.skip_snippy_multi_filter){
if(!params.skip_snippy_multi_filter && !params.skip_snippy_multi && !params.skip_snippy_merge_mask_bed && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process snippy_multi_filter{
/*
Expand Down Expand Up @@ -830,7 +831,7 @@ if(!params.skip_snippy_multi_filter){
// ML Phylogeny //
// -------------------------------------------------------------------------- //

if(!params.skip_iqtree){
if(!params.skip_iqtree && !params.skip_snippy_multi_filter && !params.skip_snippy_multi && !params.skip_snippy_merge_mask_bed && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

process iqtree{
/*
Expand Down Expand Up @@ -881,70 +882,75 @@ if(!params.skip_iqtree){
// Visualization MultiQC //
// -------------------------------------------------------------------------- //

process qualimap_snippy_pairwise{
/*
if(!params.skip_qualimap_snippy_pairwise && !params.skip_iqtree && !params.skip_snippy_multi_filter && !params.skip_snippy_multi && !params.skip_snippy_merge_mask_bed && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

Run QualiMap on the output bam of snippy pairwise.
process qualimap_snippy_pairwise{
/*
Input:
ch_snippy_bam_pairwise_qualimap (bam): Pairwise alignment file from process snippy_pairwise.
Run QualiMap on the output bam of snippy pairwise.
Output:
ch_snippy_pairwise_qualimap_multiqc (misc): All default qualimap output for process multiqc.
Input:
ch_snippy_bam_pairwise_qualimap (bam): Pairwise alignment file from process snippy_pairwise.
Publish:
* (misc): All default qualimap output.
*/
// Other variables and config
tag "${snippy_bam}"
publishDir "${outdir}/snippy_pairwise/qualimap", mode: 'copy'
Output:
ch_snippy_pairwise_qualimap_multiqc (misc): All default qualimap output for process multiqc.
// IO and conditional behavior
input:
file snippy_bam from ch_snippy_bam_pairwise_qualimap
output:
file "*" into ch_snippy_pairwise_qualimap_multiqc
Publish:
* (misc): All default qualimap output.
*/
// Other variables and config
tag "${snippy_bam}"
publishDir "${outdir}/snippy_pairwise/qualimap", mode: 'copy'

// Shell script to execute
script:
"""
qualimap bamqc -bam ${snippy_bam} --skip-duplicated -c -outformat "HTML" -outdir . -nt ${task.cpus}
qualimapDir=${snippy_bam.baseName}_stats
mv \$qualimapDir ${snippy_bam.baseName}
"""
// IO and conditional behavior
input:
file snippy_bam from ch_snippy_bam_pairwise_qualimap
output:
file "*" into ch_snippy_pairwise_qualimap_multiqc

// Shell script to execute
script:
"""
qualimap bamqc -bam ${snippy_bam} --skip-duplicated -c -outformat "HTML" -outdir . -nt ${task.cpus}
qualimapDir=${snippy_bam.baseName}_stats
mv \$qualimapDir ${snippy_bam.baseName}
"""
}
}

process multiqc{
/*
Generate a MultiQC report from pipeline analyses.
if(!params.skip_multiqc && !params.skip_qualimap_snippy_pairwise && !params.skip_iqtree && !params.skip_snippy_multi_filter && !params.skip_snippy_multi && !params.skip_snippy_merge_mask_bed && !params.skip_snippy_pairwise && !params.skip_assembly_download && (params.sqlite || params.ncbimeta_update)){

Input:
ch_snippy_pairwise_qualimap_multiqc (misc): All default qualimap output from process qualimap_snippy_pairwise.
process multiqc{
/*
Generate a MultiQC report from pipeline analyses.
Publish
multiqc_report.html (html): MultiQC report file.
*_data (misc): All default MultiQC data files.
*/
// Other variables and config
tag "${qualimap_misc}"
publishDir "${outdir}/multiqc", mode: 'copy'
Input:
ch_snippy_pairwise_qualimap_multiqc (misc): All default qualimap output from process qualimap_snippy_pairwise.
// IO and conditional behavior
input:
file qualimap_misc from ch_snippy_pairwise_qualimap_multiqc.collect()
file snpeff_misc from ch_snippy_csv_snpEff_multiqc.collect()
Publish
multiqc_report.html (html): MultiQC report file.
*_data (misc): All default MultiQC data files.
*/
// Other variables and config
tag "${qualimap_misc}"
publishDir "${outdir}/multiqc", mode: 'copy'

output:
file "*multiqc_report.html"
file "*_data"
// IO and conditional behavior
input:
file qualimap_misc from ch_snippy_pairwise_qualimap_multiqc.collect()
file snpeff_misc from ch_snippy_csv_snpEff_multiqc.collect()

// Shell script to execute
script:
"""
multiqc --config ${params.multiqc_config} .
"""
}
output:
file "*multiqc_report.html"
file "*_data"

// Shell script to execute
script:
"""
multiqc --config ${params.multiqc_config} .
"""
}
}

/* Stock process
process my_process{
Expand Down

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