Snakefile4test

import os
submit_job = config["submit_job"]
outdir_abspath = os.path.abspath(config["outdir"])

param_test_email = ""
if "test_email" in config:
    test_email = config["test_email"]
    param_test_email = f"--test-email {test_email} -y 100"

include: "rules/test_rna.smk"
include: "rules/test_multi.smk"
include: "rules/test_spatia.smk"
include: "rules/test_spatia_polyA.smk"
include: "rules/test_rna_full.smk"
include: "rules/test_vdj.smk"
include: "rules/test_multiome.smk"
include: "rules/test_atac.smk"
include: "rules/test_nopipe.smk"
include: "rules/test_fixedrna_singleplex.smk"

rule all:
    input:
        rules.test_sc_fixedrna_singleplex_default.log,
        rules.test_sc_rna_full_default.output.log,
        rules.test_sc_spatial_default.output.log,
        rules.test_sc_spatial_polyA_default.output.log,
        rules.test_sc_rna_expect_cell.output.log,
        rules.test_sc_rna_force_cell.output.log,
        rules.test_sc_rna_exclude_introns.output.log,
        rules.test_sc_rna_default.output.log,
        rules.test_sc_multi_default.output.log,
        rules.test_sc_multi_force_cell.output.log,
        rules.test_sc_multi_expect_cell.output.log,
        rules.test_sc_vdj_default.output.log,
        rules.test_sc_vdj_chain.output.log,
        rules.test_sc_multiome_default.output.log,
        rules.test_sc_multiome_exclude_exons.output.log,
        rules.test_sc_atac_default.output.log,
        rules.test_sc_nopipe_default.output.log,