Skip to content

Commit

Permalink
fixed conflicts
Browse files Browse the repository at this point in the history
  • Loading branch information
@dhspence
dhspence committed Jul 2, 2024
2 parents 686d93d + 07c6139 commit efb4287
Show file tree
Hide file tree
Showing 24 changed files with 2,836 additions and 54 deletions.
Empty file added assets/NO_FILE.bed
View file
Empty file.
Empty file added assets/NO_FILE.csv
View file
Empty file.
Empty file added assets/NO_FILE.vcf
View file
Empty file.
2,546 changes: 2,546 additions & 0 deletions assets/PDCD4_sgRNA2_combined_sites.csv
View file

Large diffs are not rendered by default.

14 changes: 14 additions & 0 deletions assets/accessory_files/example.bed
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
chr17 7669608 7669692 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_11|7669609|7676594|-1
chr17 7670606 7670717 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_10|7669609|7676594|-1
chr17 7673532 7673610 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_9|7669609|7676594|-1
chr17 7673698 7673839 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_8|7669609|7676594|-1
chr17 7673795 7673796 TP53 MSHD_hotspot|ENSG00000141510|ENST00000269305|codon_275|7669609|7676594|-1
chr17 7673801 7673803 TP53 MSHD_hotspot|ENSG00000141510|ENST00000269305|codon_273|7669609|7676594|-1
chr17 7674178 7674292 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_7|7669609|7676594|-1
chr17 7674219 7674221 TP53 MSHD_hotspot|ENSG00000141510|ENST00000269305|codon_248|7669609|7676594|-1
chr17 7674249 7674250 TP53 MSHD_hotspot|ENSG00000141510|ENST00000269305|codon_238|7669609|7676594|-1
chr17 7674856 7674973 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_6|7669609|7676594|-1
chr17 7675050 7675238 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_5|7669609|7676594|-1
chr17 7675991 7676274 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_4|7669609|7676594|-1
chr17 7676379 7676405 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_3|7669609|7676594|-1
chr17 7676518 7676594 TP53 MSHD_genes|ENSG00000141510|ENST00000269305|exon_2|7669609|7676594|-1
60 changes: 60 additions & 0 deletions assets/batch_240216_samplesheet.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,60 @@
id,uid,sample_type,read1,read2
CD34-CART-DNA,ATF71B-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
ATF71B-KO-CART,ATF71B-KO,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L005_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L005_R2_001.fastq.gz

CD34-CART-DNA,ATF71B-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
ATF71B-KO-CART,ATF71B-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L006_R2_001.fastq.gz

CD34-CART-DNA,ATF71B-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
ATF71B-KO-CART,ATF71B-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L007_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L007_R2_001.fastq.gz

CD34-CART-DNA,ATF71B-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
ATF71B-KO-CART,ATF71B-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L008_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/ATF71B-KO-CART-DNA_S5_L008_R2_001.fastq.gz

CD34-CART-DNA,BRAF-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
BRAF-KO-CART,BRAF-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L005_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L005_R2_001.fastq.gz

CD34-CART-DNA,BRAF-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
BRAF-KO-CART,BRAF-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L006_R2_001.fastq.gz

CD34-CART-DNA,BRAF-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
BRAF-KO-CART,BRAF-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L007_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L007_R2_001.fastq.gz

CD34-CART-DNA,BRAF-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
BRAF-KO-CART,BRAF-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L008_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/BRAF-KO-CART-DNA_S4_L008_R2_001.fastq.gz

CD34-CART-DNA,CHD6-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
CHD6-KO-CART,CHD6-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L005_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L005_R2_001.fastq.gz

CD34-CART-DNA,CHD6-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
CHD6-KO-CART,CHD6-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L006_R2_001.fastq.gz

CD34-CART-DNA,CHD6-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
CHD6-KO-CART,CHD6-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L007_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L007_R2_001.fastq.gz

CD34-CART-DNA,CHD6-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
CHD6-KO-CART,CHD6-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L008_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L008_R2_001.fastq.gz

CD34-CART-DNA,KDM7A-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
KDM7A-KO-CART,KDM7A-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L005_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L005_R2_001.fastq.gz

CD34-CART-DNA,KDM7A-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
KDM7A-KO-CART,KDM7A-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L006_R2_001.fastq.gz

CD34-CART-DNA,KDM7A-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
KDM7A-KO-CART,KDM7A-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L007_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L007_R2_001.fastq.gz

CD34-CART-DNA,KDM7A-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
KDM7A-KO-CART,KDM7A-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L008_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/KDM7A-KO-CART-DNA_S3_L008_R2_001.fastq.gz

CD34-CART-DNA,PDCD4-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
PDCD4-KO-CART,PDCD4-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L005_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L005_R2_001.fastq.gz

CD34-CART-DNA,PDCD4-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
PDCD4-KO-CART,PDCD4-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L006_R2_001.fastq.gz

CD34-CART-DNA,PDCD4-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
PDCD4-KO-CART,PDCD4-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L007_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L007_R2_001.fastq.gz

CD34-CART-DNA,PDCD4-KO,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
PDCD4-KO-CART,PDCD4-KO,tumor/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L008_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/PDCD4-KO-CART-DNA_S2_L008_R2_001.fastq.gz
3 changes: 3 additions & 0 deletions assets/hotspot_small.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
id,uid,sample_type,read1,read2,hotspot_file
Donor_16_Edited,Donor_16,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_R2_001.fastq.gz,
Donor_16_Unedited,Donor_16,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R2_001.fastq.gz,
11 changes: 11 additions & 0 deletions assets/hotspot_test.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
id,uid,sample_type,read1,read2,hotspot_file
Donor_16_Edited_L005_R1_001,Donor_16,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L005_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L005_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Unedited,Donor_16,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Edited_L006_R1_001,Donor_16_2,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L006_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Unedited,Donor_16_2,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Edited_L007_R1_001,Donor_16_3,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L007_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L007_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Unedited,Donor_16_3,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Edited_L008_R1_001,Donor_16_4,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L008_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_L008_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Unedited,Donor_16_4,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Edited,Donor_16_5,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Edited-DNA_S2_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Unedited,Donor_16_5,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/CLE-5280/test_fastq/Donor_16_Unedited-DNA_S1_L006_R2_001.fastq.gz,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
3 changes: 3 additions & 0 deletions assets/stub/cram_test.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
id,uid,sample_type,cram,hotspot_file
Donor_16_Unedited,Donor_16,normal,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/stub/crams/Donor_16_CART.cram,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Donor_16_Edited,Donor_16,tumor,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/stub/crams/Donor_16_CART_tumor.cram,/storage1/fs1/dspencer/Active/spencerlab/dnidhi/pipelines/git_runs/scge/nf-core-scge/assets/PDCD4_sgRNA2_combined_sites.csv
Empty file modified assets/stub/demux_fastq/.dir_bash_history
100755 → 100644
View file
Empty file.
Empty file modified assets/stub/dragen_path/.dir_bash_history
100755 → 100644
View file
Empty file.
3 changes: 3 additions & 0 deletions assets/stub/read_test.csv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
id,uid,sample_type,read1,read2
CD34-CART-DNA,CHD6-KO-CART,normal,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CD34-CART-DNA_S6_L003_R2_001.fastq.gz
CHD6-KO-CART-DNA,CHD6-KO-CART,tumor,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L005_R1_001.fastq.gz,/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/batch_240216/demux_fastq/CHD6-KO-CART-DNA_S1_L005_R2_001.fastq.gz
5 changes: 2 additions & 3 deletions assets/test_samplesheet.csv
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,2 @@
sample,single_end,fastq_1,fastq_2
SAMPLE1_PE_T1,False,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz
SAMPLE2_PE_T1,False,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz
id,dragen_path
Donor_16_CART,/storage1/fs1/dspencer/Active/clinseq/projects/scge/workflow/sample_data/Donor_16_CART
4 changes: 2 additions & 2 deletions bin/getIndelsFromBam.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -218,8 +218,8 @@ def get_indels(bam,chr,start,end,pampos,strand,srchSeq,srchSeqMM):
bed = args.bed

# open bam file(s)
expsamfile = pysam.AlignmentFile(args.expbamfile,"rc",reference_filename="/storage1/fs1/dspencer/Active/clinseq/projects/scge/cart_seq/refdata/singh/hg38_PLVM_CD19_CARv4_cd34.fa")
consamfile = pysam.AlignmentFile(args.conbamfile,"rc",reference_filename="/storage1/fs1/dspencer/Active/clinseq/projects/scge/cart_seq/refdata/singh/hg38_PLVM_CD19_CARv4_cd34.fa")
expsamfile = pysam.AlignmentFile(args.expbamfile,"rc",reference_filename="/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/refdata/singh/hg38_PLVM_CD19_CARv4_cd34.fa")
consamfile = pysam.AlignmentFile(args.conbamfile,"rc",reference_filename="/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/refdata/singh/hg38_PLVM_CD19_CARv4_cd34.fa")

distup = 20
distdown = 20
Expand Down
2 changes: 1 addition & 1 deletion bin/getTransgeneJunctions.v2.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ def get_chimeras(bam,contig,exclude=None,minSoftClip=20,minMq=1,maxMismatches=1)
contig = args.contig

# open bam file(s)
expsamfile = pysam.AlignmentFile(args.expbamfile,"rc",reference_filename="/storage1/fs1/dspencer/Active/clinseq/projects/scge/cart_seq/refdata/singh/hg38_PLVM_CD19_CARv4_cd34.fa")
expsamfile = pysam.AlignmentFile(args.expbamfile,"rc",reference_filename="/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/refdata/singh/hg38_PLVM_CD19_CARv4_cd34.fa")

chimericReads = get_chimeras(expsamfile,contig,exclude=args.exclude)

Expand Down
Loading

0 comments on commit efb4287

Please sign in to comment.