complete migration of whitelists to chemistry yaml, add zsh to conda yaml, set shell executable to zsh in PATH

Author: agillen

Snakefile

@@ -1,4 +1,4 @@
-shell.executable("/bin/zsh")
+shell.executable("zsh")
 
 """ Snakemake pipeline for single-cell RNA-seq 3' end counting """
 
@@ -8,8 +8,6 @@ DATA = config["DATA"]
 RESULTS = config["RESULTS"]
 STAR_INDEX = config["STAR_INDEX"]
 POLYA_SITES = config["POLYA_SITES"]
-WHITELIST_V2 = config["WHITELIST_V2"]
-WHITELIST_V3 = config["WHITELIST_V3"]
 STAR = config["STAR"]
 DEFAULTS = config["DEFAULTS"]
 SAMPLES = config["SAMPLES"]

chemistry.yaml

@@ -10,7 +10,7 @@
 #     STAR_R2: ...
 
 chromiumV3:
-  bc_whitelist: "ref/3M-february-2018.txt"
+  bc_whitelist: ref/3M-february-2018.txt
   illumina:
     cutadapt_paired: -a TSO_R1=CCCATGTACTCTGCGTTGATACCACTGCTT -a TruSeq_R1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A polya_R2=A{30} -G TSO_R2=XAAGCAGTGGTATCAACGCAGAGTACATGGG -n 4 -m 75:17 --nextseq-trim=20
     cutadapt_R1: -a TSO_R1=CCCATGTACTCTGCGTTGATACCACTGCTT -a TruSeq_R1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -n 2 -m 75 -l 300 --nextseq-trim=20
@@ -25,7 +25,7 @@ chromiumV3:
     cutadapt_R1: -a 'CTACACGACGCTCTTCCGATCT;max_error_rate=0.2;min_overlap=10;required...AGATCGGAAGAGCACACGTCTG;max_error_rate=0.2;min_overlap=6' -a TSO_R1=CCCATGTACTCTGCGTTGATACCACTGCTT -n 2 -m 68 -q 20
     STAR_R1: --soloUMIlen 9 --clip5pNbases 38 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17
 chromiumV2:
-  bc_whitelist: "ref/737K-august-2016.txt"
+  bc_whitelist: ref/737K-august-2016.txt
   illumina:
     cutadapt_paired: -a TSO_R1=CCCATGTACTCTGCGTTGATACCACTGCTT -a TruSeq_R1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A polya_R2=A{30} -G TSO_R2=XAAGCAGTGGTATCAACGCAGAGTACATGGG -n 4 -m 75:17 --nextseq-trim=20
     STAR_R1: --soloUMIlen 10 --clip5pNbases 46 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --outFilterMultimapNmax 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.2

rules/cutadapt_star.snake

@@ -26,7 +26,7 @@ def _get_bc_cut(wildcards):
 """ Extract per-capture chemistry from gex libs (base function) """
 def _get_chem_version(sample, alignment):
     try:
-      whitelist = eval(_get_config(sample, "bc_whitelist"))
+      whitelist = _get_config(sample, "bc_whitelist")
     except KeyError:
       whitelist = "None"
     try:

scraps_conda.yml

@@ -15,3 +15,4 @@ dependencies:
   - subread >= 2.0.1
   - umi_tools >= 1.1.2
   - star >= 2.7.9a
+  - zsh