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Implement new pooled mixed-mode default behavior #454

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merged 2 commits into from
Jul 15, 2024
Merged

Implement new pooled mixed-mode default behavior #454

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47531e0
changes for pooled mixed-mode default (#83)
mbowcut2 Jul 12, 2024
96432ba
Revert change to pooled mixed mode info statement (#86)
Colelyman Jul 15, 2024
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26 changes: 18 additions & 8 deletions .github/workflows/integration_tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -49,39 +49,49 @@ jobs:

- name: Run Basic
run: |
make basic test
make basic test print

- name: Run Params
if: success() || failure()
run: |
make params test
make params test print

- name: Run Prime Editor
if: success() || failure()
run: |
make prime-editor test
make prime-editor test print

- name: Run Batch
if: success() || failure()
run: |
make batch test
make batch test print

- name: Run Pooled
if: success() || failure()
run: |
make pooled test
make pooled test print

- name: Run Pooled Mixed Mode
if: success() || failure()
run: |
make pooled-mixed-mode test print

- name: Run Pooled Mixed Mode Demux
if: success() || failure()
run: |
make pooled-mixed-mode-genome-demux test print

- name: Run Pooled Paired Sim
if: success() || failure()
run: |
make pooled-paired-sim test
make pooled-paired-sim test print

- name: Run WGS
if: success() || failure()
run: |
make wgs test
make wgs test print

- name: Run Compare
if: success() || failure()
run: |
make compare test
make compare test print
2 changes: 1 addition & 1 deletion CRISPResso2/CRISPRessoPooledCORE.py
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Expand Up @@ -1032,7 +1032,7 @@ def rreplace(s, old, new):
os.mkdir(MAPPED_REGIONS)

# if we should only demultiplex where amplicons aligned... (as opposed to the whole genome)
if RUNNING_MODE=='AMPLICONS_AND_GENOME' and args.demultiplex_only_at_amplicons:
if RUNNING_MODE=='AMPLICONS_AND_GENOME' and not args.demultiplex_genome_wide:
s1 = r'''samtools view -F 0x0004 %s __REGIONCHR__:__REGIONSTART__-__REGIONEND__ 2>>%s |''' % (bam_filename_genome, log_filename)+\
r'''awk 'BEGIN{OFS="\t";num_records=0;fastq_filename="__OUTPUTPATH__REGION___REGIONCHR_____REGIONSTART_____REGIONEND__.fastq";} \
{ \
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