Added salmon quantification logic.

sc-preprocess.snake

@@ -41,6 +41,9 @@ if config["action"]["clean"]:
   clean_files = expand('{o}/{s}.clean.fastq.gz', o = config['dirs']['fastq'], s = SAMPLE_NAMES)
   output_files.extend(clean_files)
 
+quant_files = expand('{o}/{s}/quant.sf', o = config['dirs']['quant'], s = SAMPLE_NAMES)
+output_files.extend(quant_files)
+
 #-------------------------------------------------------------------------------#
 #---------------------------------- RUN :-) ------------------------------------#
 #-------------------------------------------------------------------------------#
@@ -49,6 +52,7 @@ include: "src/auxiliary.snake"
 #include: "src/demultiplex.snake" # not yet implemented
 include: "src/reference.snake"
 include: "src/clean.snake"
+include: "src/salmon.snake"
 
 if config["debug"]:
   print_debug()

src/salmon.snake

@@ -0,0 +1,51 @@
+# vim: syntax=python tabstop=4 expandtab
+# coding: utf-8
+
+'''
+@author: jpreuss
+
+Provides Salmon alignment-free quantification
+'''
+
+SALMON_VERSION = subprocess.check_output("salmon -v", shell=True)
+
+rule salmon_index:
+  input:
+    REFERENCE_FASTA
+  output:
+    join(config['dirs']['ref'], 'salmon', basename(REFERENCE_FASTA).rstrip(".fa"))
+  threads: 30
+  params:
+    flags = config['salmon']['index_flags'] if 'index_flags' in config.get('salmon', {}) else ''
+  log:
+    'logs/salmon_index.log'
+  message: 'Creating Salmon index for {input}.'
+  version: SALMON_VERSION
+  shell:
+    """
+    salmon index -p {threads} -t {input} -i {output} {params.flags} &> {log}
+    """
+
+def salmon_input_r1(wildcards):
+  if config['action']['clean']:
+    return('{o}/{s}.clean.fastq.gz'.format(o = config['dirs']['fastq'], s = wildcards.sample))
+  else:
+    return(SAMPLES[wildcards.sample]['URL_r1'])
+
+rule salmon_quant_se:
+  input:
+    r1 = salmon_input_r1,
+    index = rules.salmon_index.output
+  output:
+    config['dirs']['quant'] + '/{sample}/quant.sf'
+  params:
+    flags = config['salmon']['quant_flags'] if 'quant_flags' in config.get('salmon', {}) else ''
+  log:
+    'logs/salmon_quant_{sample}.log'
+  message: 'Quantifying {wildcards.sample} with Salmon using {threads} threads.'
+  threads: 30
+  version: SALMON_VERSION
+  shell:
+    """
+    salmon quant -p {threads} -i {input.index} -l ISR -r {input.r1} -o {config[dirs][quant]}/{wildcards.sample} {params.flags} &> {log}
+    """