adding claireS

mop_dna/mop_dna.nf

@@ -43,8 +43,7 @@ if (params.help) exit 1
 if (params.resume) exit 1, "Are you making the classical --resume typo? Be careful!!!! ;)"
 
 // check input files
-reference = file(params.reference)
-if( !reference.exists() ) exit 1, "Missing reference file: ${reference}!"
+reference = channel.fromPath(params.reference, checkIfExists: true)
 
 // include functions, outdirs from other files
 evaluate(new File("../outdirs.nf"))
@@ -63,6 +62,8 @@ include { checkRef } from "${local_modules}"
 progPars = getParameters(params.pars_tools)
 
 include { RUN as RUN_CLAIRS } from "${subworkflowsDir}/snp_calling/clairS" addParams(LABEL: 'big_mem_cpus', EXTRAPARS: progPars["clairS--clairS"], OUTPUT: outputClairS)
+include { CHECK_FASTA } from "${subworkflowsDir}/misc/misc.nf"
+include { FAIDX as SAMTOOLS_FAIDX } from "${subworkflowsDir}/misc/samtools" 
 
 
 
@@ -104,8 +105,9 @@ workflow {
          [it, file("${params.input_path}/alignment/${it}_s.bam.bai")]
     }.transpose().set{bais}
 
-   // ref_file = checkRef(reference)
-   clairS_flow(bams, comparisons, reference)
+   checked_genome = CHECK_FASTA(reference)
+   faidx = SAMTOOLS_FAIDX(checked_genome)
+   clairS_flow(bams, bais, comparisons, checked_genome, faidx)
 
 
 }
@@ -115,12 +117,23 @@ workflow clairS_flow {
 
     take:
     bam
+    bais
     comparisons
     reference
+    faidx
 
     main:
-    data = mapIDPairs(comparisons, bam)
-    RUN_CLAIRS(data, reference)
+    bam_comp = mapIDPairs(comparisons, bam).map{
+    	[ "${it[0]}--${it[1]}", it[2], it[3] ]  
+    }
+
+
+    bai_comp = mapIDPairs(comparisons, bais).map{
+    	[ "${it[0]}--${it[1]}", it[2], it[3] ]  
+    }
+
+    data = bam_comp.join(bai_comp)    
+    RUN_CLAIRS(data, reference, faidx)
 
 //    emit:
 

mop_dna/params.yaml

@@ -1,6 +1,7 @@
 input_path: "${projectDir}/test_dataset/"
 comparison: "${projectDir}/comparison.tsv"
 
+##reference: "${projectDir}/GRCh38.primary_assembly.genome.fa"
 reference: "/db/gencode/human/release_38/GRCh38.primary_assembly.genome.fa.gz"
 output: "${projectDir}/output_dna"
 pars_tools: "${projectDir}/tools_opt.tsv"

outdirs.nf

@@ -19,6 +19,9 @@ outputNanoPolComFlow = "${params.output}/nanopolish-compore_flow"
 outputTomboFlow      = "${params.output}/tombo_flow"
 outputModPhredFlow   = "${params.output}/modphred_flow"
 
+// mop_dna
+outputClairS         = "${params.output}/clairS_flow"
+
 // MOP_TAIL
 outputTailFindr     = "${params.output}/tailfindr_flow"
 outputNanopolish    = "${params.output}/nanopolish_flow"