@@ -5,14 +5,12 @@ date = new Date().format( 'yyyyMMdd' )
55
66
77log. info """ \
8- L O G A N P I P E L I N E
8+ L O G A N P I P E L I N E
99 =============================
1010 genome: ${ params.genome}
1111 outdir: ${ params.outdir}
1212 Sample Sheet: ${ params.sample_sheet}
13- Samples: ${ params.fastq_input} ${ params.file_input} ${ params.bam_input}
14- NF version : $nextflow . version
15-
13+ Samples: ${ params.fastq_input} ${ params.fastq_file_input} ${ params.bam_input} ${ params.bam_file_input}
1614 """
1715 .stripIndent()
1816
@@ -40,8 +38,7 @@ workflow.onComplete {
4038
4139// Final Workflow
4240workflow {
43- DETERMINEBAM ()
44- if ([params. fastq_input,params. file_input]. any() && params. sample_sheet && ! params. BAMINPUT ){
41+ if ([params. fastq_input,params. fastq_file_input]. any() && params. sample_sheet){
4542 println " Tumor-Normal FASTQ"
4643 INPUT ()
4744 ALIGN (INPUT . out. fastqinput,INPUT . out. sample_sheet)
@@ -52,10 +49,10 @@ workflow {
5249 // Tumor-Normal VC, SV, CNV
5350 if (params. vc){
5451 VC (ALIGN . out. bamwithsample,ALIGN . out. splitout,ALIGN . out. sample_sheet)
55- }
52+ }
5653 if (params. sv){
5754 SV (ALIGN . out. bamwithsample)
58- }
55+ }
5956 if (params. cnv){
6057 if (params. genome == " mm10"
6158 CNVmouse (ALIGN . out. bamwithsample)
@@ -67,41 +64,41 @@ workflow {
6764 CNVhuman (ALIGN . out. bamwithsample,VC . out. somaticcall_input)
6865 }
6966 }
70- }
67+ }
7168 if (params. qc && params. gl){
7269 QC_GL (ALIGN . out. fastqin,ALIGN . out. fastpout,ALIGN . out. bqsrout,GL . out. glnexusout,GL . out. bcfout)
7370 } else if (params. qc){
7471 QC_NOGL (ALIGN . out. fastqin,ALIGN . out. fastpout,ALIGN . out. bqsrout)
75- }
72+ }
7673
7774 }
78-
75+
7976 // TUMOR-NOMRAL BAM INPUT
80- if ([params. bam_input,params. file_input ]. any() && params. sample_sheet && BAMINPUT ){
77+ if ([params. bam_input,params. bam_file_input ]. any() && params. sample_sheet){
8178 println " Tumor-Normal with BAMs"
8279 INPUT_BAM ()
8380 if (params. vc){
8481 VC (INPUT_BAM . out. bamwithsample,INPUT_BAM . out. splitout,INPUT_BAM . out. sample_sheet)
85- }
82+ }
8683 if (params. sv){
8784 SV (INPUT_BAM . out. bamwithsample)
88- }
85+ }
8986 if (params. cnv){
9087 if (params. genome == " mm10"
9188 CNVmouse (INPUT_BAM . out. bamwithsample)
9289 } else if (params. genome== " hg38"
9390 if (! params. vc){
9491 VC (INPUT_BAM . out. bamwithsample,INPUT_BAM . out. splitout,INPUT_BAM . out. sample_sheet)
9592 CNVhuman (INPUT_BAM . out. bamwithsample,VC . out. somaticcall_input)
96- }else {
93+ }else {
9794 CNVhuman (INPUT_BAM . out. bamwithsample,VC . out. somaticcall_input)
9895 }
9996 }
10097 }
101- }
102-
98+ }
99+
103100 // /Tumor Only Pipelines
104- if ([params. fastq_input,params. file_input]. any() && ! params. sample_sheet && ! params . BAMINPUT ){
101+ if ([params. fastq_input,params. file_input]. any() && ! params. sample_sheet){
105102 println " Tumor-Only FASTQ"
106103 INPUT_TONLY ()
107104 ALIGN_TONLY (INPUT_TONLY . out. fastqinput,INPUT_TONLY . out. sample_sheet)
@@ -118,7 +115,7 @@ workflow {
118115 if (! params. vc){
119116 VC_TONLY (ALIGN_TONLY . out. bamwithsample,ALIGN_TONLY . out. splitout,ALIGN_TONLY . out. sample_sheet)
120117 CNVhuman_tonly (ALIGN_TONLY . out. bamwithsample,VC_TONLY . out. somaticcall_input)
121- } else {
118+ } else {
122119 CNVhuman_tonly (ALIGN_TONLY . out. bamwithsample,VC_TONLY . out. somaticcall_input)
123120 }
124121 }
@@ -129,28 +126,27 @@ workflow {
129126 }
130127
131128 // Variant Calling from BAM-Tumor Only Mode
132- if ([params. bam_input,params. file_input ]. any() && ! params. sample_sheet && params . BAMINPUT ){
129+ if ([params. bam_input,params. bam_file_input ]. any() && ! params. sample_sheet){
133130 println " Tumor-Only BAM"
134131 INPUT_TONLY_BAM ()
135132 if (params. vc){
136133 VC_TONLY (INPUT_TONLY_BAM . out. bamwithsample,INPUT_TONLY_BAM . out. splitout,INPUT_TONLY_BAM . out. sample_sheet)
137134 }
138135 if (params. sv){
139136 SV_TONLY (INPUT_TONLY_BAM . out. bamwithsample)
140- }
137+ }
141138 if (params. cnv){
142139 if (params. genome == " mm10"
143140 CNVmouse_tonly (INPUT_TONLY_BAM . out. bamwithsample)
144141 } else if (params. genome== " hg38"
145- VC_TONLY ( INPUT_TONLY_BAM . out . bamwithsample, INPUT_TONLY_BAM . out . splitout, INPUT_TONLY_BAM . out . sample_sheet)
146- CNVhuman_tonly (INPUT_TONLY_BAM . out. bamwithsample,VC_TONLY . out. somaticcall_input )
147- }
148- }
149-
150- }
142+ if ( ! params . vc){
143+ VC_TONLY (INPUT_TONLY_BAM . out. bamwithsample,INPUT_TONLY_BAM . out. splitout, INPUT_TONLY_BAM . out . sample_sheet )
144+ CNVhuman_tonly ( INPUT_TONLY_BAM . out . bamwithsample, VC_TONLY . out . somaticcall_input)
145+ } else {
146+ CNVhuman_tonly ( INPUT_TONLY_BAM . out . bamwithsample, VC_TONLY . out . somaticcall_input)
147+ }
151148
149+ }
150+ }
151+ }
152152}
153-
154-
155-
156-
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