|
|
|
|
|
|
|
|
input: |
|
|
input: |
|
|
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, |
|
|
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, |
|
|
SENTIEON_LICENSE=SENTIEON_LICENSE, |
|
|
SENTIEON_LICENSE=SENTIEON_LICENSE, |
|
|
sample=sample_id, |
|
|
|
|
|
|
|
|
sample=sample_id + '.N', |
|
|
fasta=fasta, |
|
|
fasta=fasta, |
|
|
ref_dir=ref_dir, |
|
|
ref_dir=ref_dir, |
|
|
recaled_bam=normal_BQSR.recaled_bam, |
|
|
recaled_bam=normal_BQSR.recaled_bam, |
|
|
|
|
|
|
|
|
if (pindel) { |
|
|
if (pindel) { |
|
|
call Pindel.Pindel as Pindel { |
|
|
call Pindel.Pindel as Pindel { |
|
|
input: |
|
|
input: |
|
|
sample_id=sample_id, |
|
|
|
|
|
|
|
|
sample_id=sample_id + '.N', |
|
|
bam=normal_BQSR.recaled_bam, |
|
|
bam=normal_BQSR.recaled_bam, |
|
|
bam_index=normal_BQSR.recaled_bam_index, |
|
|
bam_index=normal_BQSR.recaled_bam_index, |
|
|
fasta=fasta, |
|
|
fasta=fasta, |
|
|
|
|
|
|
|
|
input: |
|
|
input: |
|
|
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, |
|
|
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, |
|
|
SENTIEON_LICENSE=SENTIEON_LICENSE, |
|
|
SENTIEON_LICENSE=SENTIEON_LICENSE, |
|
|
sample=sample_id, |
|
|
|
|
|
|
|
|
sample=sample_id + '.N', |
|
|
fasta=fasta, |
|
|
fasta=fasta, |
|
|
ref_dir=ref_dir, |
|
|
ref_dir=ref_dir, |
|
|
recaled_bam=normal_BQSR_fb.recaled_bam, |
|
|
recaled_bam=normal_BQSR_fb.recaled_bam, |
|
|
|
|
|
|
|
|
if (pindel) { |
|
|
if (pindel) { |
|
|
call Pindel.Pindel as Pindel_fb { |
|
|
call Pindel.Pindel as Pindel_fb { |
|
|
input: |
|
|
input: |
|
|
sample_id=sample_id, |
|
|
|
|
|
|
|
|
sample_id=sample_id + '.N', |
|
|
bam=normal_BQSR_fb.recaled_bam, |
|
|
bam=normal_BQSR_fb.recaled_bam, |
|
|
bam_index=normal_BQSR_fb.recaled_bam_index, |
|
|
bam_index=normal_BQSR_fb.recaled_bam_index, |
|
|
fasta=fasta, |
|
|
fasta=fasta, |