<commit_before>_author__ = "<NAME> (<EMAIL>)"
__license__ = "MIT"
__date__ = "2015-04-22"

from snakemake.exceptions import MissingInputException
import os

rule:
    version: 0.3

localrules:
    all, run_kallisto, run_STAR, run_htseq, run_cutadapt

wrapper_dir = os.environ['HOME'] + "/Development/snakemake-wrappers/bio"

include_prefix= os.environ['HOME'] + "/Development/JCSMR-Tremethick-Lab/Breast/snakemake/rules/"

include:
    include_prefix + "run_kallisto.py"

rule run_kallisto:
    input:
        expand("{assayID}/{runID}/{outdir}/{reference_version}/kallisto/{unit}",
               assayID = "RNA-Seq",
               runID = ["NB501086_0114_B_Azad_JCSMR_hRNAseq", "NB501086_0082_RDomaschenz_JCSMR_mRNAseq"],
               outdir = config["processed_dir"],
               reference_version = "GRCh37_hg19_ensembl75",
               unit = config["samples"]["RNA-Seq"])<commit_msg>fixes expansion of targets for kallisto<commit_after>from snakemake.exceptions import MissingInputException
import os

_author__ = "<NAME> (<EMAIL>)"
__license__ = "MIT"
__date__ = "2015-04-22"

rule:
    version: 0.3

localrules:
    all, run_kallisto, run_STAR, run_htseq, run_cutadapt

wrapper_dir = os.environ['HOME'] + "/Development/snakemake-wrappers/bio"

include_prefix= os.environ['HOME'] + "/Development/JCSMR-Tremethick-Lab/Breast/snakemake/rules/"

include:
    include_prefix + "run_kallisto.py"

# variables
REF_VERSION = "GRCh37_hg19_ensembl75"

# targets
BEARS = expand("{assayID}/{file}",
              assayID = "RNA-Seq",
              file = [ i + "/" + config["processed_dir"] + "/" + REF_VERSION + "/kallisto/" + j \
                  for i in config["samples"]["ChIP-Seq"]["runID"] \
                      for j in config["samples"]["ChIP-Seq"][i]].keys())

rule run_kallisto:
    input:
        BEARS
{'fraction_non_alphanumeric': 0.14222954420647996, 'fraction_numerical': 0.028555738605161998, 'mean_word_length': 3.4876847290640396, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6810431', 'n_tokens_mistral': 714, 'n_tokens_neox': 657, 'n_words': 107}