Skip to content

Commit 7dde9e1

Browse files
ManavalanGManavalanG
authored
Merge pull request #97 from uab-cgds-worthey/parabricks
Updates QuaC to use with Parabricks pipeline output
2 parents e4a8cdd + 0892cce commit 7dde9e1

35 files changed

+398
-1010
lines changed

‎.github/workflows/draft-pdf.yml‎

Lines changed: 0 additions & 23 deletions
This file was deleted.

‎.test/configs/include_priorQC/sample_config/project_2samples_exome.tsv‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
1-
sample_id bam vcf capture_bed fastqc_raw fastqc_trimmed fastq_screen dedup multiqc_rename_config
2-
A .test/ngs-data/test_project/analysis/A/bam/A.bam .test/ngs-data/test_project/analysis/A/vcf/A.vcf.gz .test/ngs-data/test_project/analysis/A/configs/small_variant_caller/capture_regions.bed .test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R2_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-2-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-2-R2_screen.txt .test/ngs-data/test_project/analysis/A/qc/dedup/A-1.metrics.txt,.test/ngs-data/test_project/analysis/A/qc/dedup/A-2.metrics.txt .test/ngs-data/test_project/analysis/A/qc/multiqc_initial_pass/multiqc_sample_rename_config/A_rename_config.tsv
3-
B .test/ngs-data/test_project/analysis/B/bam/B.bam .test/ngs-data/test_project/analysis/B/vcf/B.vcf.gz .test/ngs-data/test_project/analysis/B/configs/small_variant_caller/capture_regions.bed .test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-1-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-1-R2_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-2-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-2-R2_screen.txt .test/ngs-data/test_project/analysis/B/qc/dedup/B-1.metrics.txt,.test/ngs-data/test_project/analysis/B/qc/dedup/B-2.metrics.txt .test/ngs-data/test_project/analysis/B/qc/multiqc_initial_pass/multiqc_sample_rename_config/B_rename_config.tsv
1+
sample_id bam vcf capture_bed fastqc fastq_screen dedup multiqc_rename_config
2+
A .test/ngs-data/test_project/analysis/A/bam/A.bam .test/ngs-data/test_project/analysis/A/vcf/A.vcf.gz .test/ngs-data/test_project/analysis/A/configs/small_variant_caller/capture_regions.bed .test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R2_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-2-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-2-R2_screen.txt .test/ngs-data/test_project/analysis/A/qc/dedup/A-1.metrics.txt,.test/ngs-data/test_project/analysis/A/qc/dedup/A-2.metrics.txt .test/ngs-data/test_project/analysis/A/qc/multiqc_initial_pass/multiqc_sample_rename_config/A_rename_config.tsv
3+
B .test/ngs-data/test_project/analysis/B/bam/B.bam .test/ngs-data/test_project/analysis/B/vcf/B.vcf.gz .test/ngs-data/test_project/analysis/B/configs/small_variant_caller/capture_regions.bed .test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-1-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-1-R2_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-2-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-2-R2_screen.txt .test/ngs-data/test_project/analysis/B/qc/dedup/B-1.metrics.txt,.test/ngs-data/test_project/analysis/B/qc/dedup/B-2.metrics.txt .test/ngs-data/test_project/analysis/B/qc/multiqc_initial_pass/multiqc_sample_rename_config/B_rename_config.tsv

‎.test/configs/include_priorQC/sample_config/project_2samples_wgs.tsv‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
1-
sample_id bam vcf fastqc_raw fastqc_trimmed fastq_screen dedup multiqc_rename_config
2-
A .test/ngs-data/test_project/analysis/A/bam/A.bam .test/ngs-data/test_project/analysis/A/vcf/A.vcf.gz .test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-trimmed/A-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R2_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-2-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-2-R2_screen.txt .test/ngs-data/test_project/analysis/A/qc/dedup/A-1.metrics.txt,.test/ngs-data/test_project/analysis/A/qc/dedup/A-2.metrics.txt .test/ngs-data/test_project/analysis/A/qc/multiqc_initial_pass/multiqc_sample_rename_config/A_rename_config.tsv
3-
B .test/ngs-data/test_project/analysis/B/bam/B.bam .test/ngs-data/test_project/analysis/B/vcf/B.vcf.gz .test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-trimmed/B-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-1-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-1-R2_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-2-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-trimmed/B-2-R2_screen.txt .test/ngs-data/test_project/analysis/B/qc/dedup/B-1.metrics.txt,.test/ngs-data/test_project/analysis/B/qc/dedup/B-2.metrics.txt .test/ngs-data/test_project/analysis/B/qc/multiqc_initial_pass/multiqc_sample_rename_config/B_rename_config.tsv
1+
sample_id bam vcf fastqc fastq_screen dedup multiqc_rename_config
2+
A .test/ngs-data/test_project/analysis/A/bam/A.bam .test/ngs-data/test_project/analysis/A/vcf/A.vcf.gz .test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/A/qc/fastqc-raw/A-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R2_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-2-R1_screen.txt,.test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-2-R2_screen.txt .test/ngs-data/test_project/analysis/A/qc/dedup/A-1.metrics.txt,.test/ngs-data/test_project/analysis/A/qc/dedup/A-2.metrics.txt .test/ngs-data/test_project/analysis/A/qc/multiqc_initial_pass/multiqc_sample_rename_config/A_rename_config.tsv
3+
B .test/ngs-data/test_project/analysis/B/bam/B.bam .test/ngs-data/test_project/analysis/B/vcf/B.vcf.gz .test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-1-R2_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R1_fastqc.zip,.test/ngs-data/test_project/analysis/B/qc/fastqc-raw/B-2-R2_fastqc.zip .test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-1-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-1-R2_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-2-R1_screen.txt,.test/ngs-data/test_project/analysis/B/qc/fastq_screen-raw/B-2-R2_screen.txt .test/ngs-data/test_project/analysis/B/qc/dedup/B-1.metrics.txt,.test/ngs-data/test_project/analysis/B/qc/dedup/B-2.metrics.txt .test/ngs-data/test_project/analysis/B/qc/multiqc_initial_pass/multiqc_sample_rename_config/B_rename_config.tsv

.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R1_screen.png renamed to .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R1_screen.png

File renamed without changes.

.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R1_screen.txt renamed to .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R1_screen.txt

File renamed without changes.

.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R2_screen.png renamed to .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R2_screen.png

File renamed without changes.

.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-1-R2_screen.txt renamed to .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-1-R2_screen.txt

File renamed without changes.

.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-2-R1_screen.png renamed to .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-2-R1_screen.png

File renamed without changes.

.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-2-R1_screen.txt renamed to .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-2-R1_screen.txt

File renamed without changes.

.test/ngs-data/test_project/analysis/A/qc/fastq_screen-trimmed/A-2-R2_screen.png renamed to .test/ngs-data/test_project/analysis/A/qc/fastq_screen-raw/A-2-R2_screen.png

File renamed without changes.

0 commit comments

Comments
 (0)