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* turns out test data project_df.csv was hard-wired to paths on marga…
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…ret. Modified to be relative to spacemake source
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Marvin Jens committed Jan 26, 2024
1 parent 99d18a2 commit cd5e26e
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Showing 2 changed files with 12 additions and 8 deletions.
14 changes: 7 additions & 7 deletions test_data/test_project_df.csv
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
project_id,sample_id,puck_barcode_file_id,sample_sheet,species,demux_barcode_mismatch,demux_dir,basecalls_dir,R1,R2,reads,longreads,longread_signature,investigator,sequencing_date,experiment,puck_barcode_file,run_mode,barcode_flavor,is_merged,merged_from,puck,dge,map_strategy,adapter_flavor
test,test_01,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
test,test_01b,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
test,test_02,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
test,test_03_nofinal,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR,dropseq
tile,tile_1,['tile_1'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_1.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
tile,tile_2,['tile_2'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_2.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
tile,tile_both,"['tile_1', 'tile_2']",,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,"['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_1.txt', '/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_2.txt']",['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
test,test_01,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
test,test_01b,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
test,test_02,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
test,test_03_nofinal,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR,dropseq
tile,tile_1,['tile_1'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['{spacemake_dir}/test_data/tile_1.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
tile,tile_2,['tile_2'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['{spacemake_dir}/test_data/tile_2.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
tile,tile_both,"['tile_1', 'tile_2']",,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,"['{spacemake_dir}/test_data/tile_1.txt', '{spacemake_dir}/test_data/tile_2.txt']",['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
6 changes: 5 additions & 1 deletion tests/fixtures.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import os

spacemake_dir = os.path.abspath(os.path.dirname(__file__) + '/../')
print("SPACEMAKE_DIR", spacemake_dir)

def sm(*argc, expect_fail=False):
# construct the desired cmdline
Expand Down Expand Up @@ -120,7 +121,10 @@ def configured_root(tmp_path_factory):
os.system(f"cp {def_config} {tmp_root / 'config.yaml'}")

test_pdf = os.path.join(sm_path, "../test_data/test_project_df.csv")
os.system(f"cp {test_pdf} {tmp_root / 'project_df.csv'}")
open(f"{tmp_root / 'project_df.csv'}", 'w').write(
open(test_pdf, 'r').read().format(spacemake_dir=spacemake_dir)
)
#os.system(f"cp {test_pdf} {tmp_root / 'project_df.csv'}")

return tmp_root

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