use shadow keyword correctly #137. Make kallisto multithreaded. Correct TIN score multithreading.

Snakefile

@@ -166,7 +166,7 @@ rule fastqc:
 
     shell:
         "(mkdir -p {output.outdir}; \
-        fastqc --outdir {output.outdir} {input.reads}) \
+        fastqc --outdir {output.outdir} --threads {threads} {input.reads}) \
         1> {log.stdout} 2> {log.stderr}"
 
 
@@ -345,8 +345,6 @@ rule create_index_salmon:
                 "{kmer}",
                 "salmon.idx"))
 
-    shadow: "full"
-
     params:
         kmerLen = "{kmer}"
 
@@ -531,8 +529,6 @@ rule calculate_TIN_scores:
             "TIN",
             "TIN_score.tsv"))
 
-    shadow: "full"
-
     params:
         sample = "{sample}"
 
@@ -554,7 +550,7 @@ rule calculate_TIN_scores:
         -r {input.transcripts_bed12} \
         -c 0 \
         --names {params.sample} \
-        -n 100 > {output.TIN_score};) 2> {log.stderr}"
+        -n {threads} > {output.TIN_score};) 2> {log.stderr}"
 
 
 rule merge_TIN_scores:
@@ -1126,8 +1122,6 @@ rule generate_alfa_index:
             "ALFA",
             "sorted_genes.unstranded.ALFA_index")
 
-    shadow: "full"
-
     params:
         genome_index = "sorted_genes",
         out_dir = lambda wildcards, output:

workflow/rules/paired_end.snakefile.smk

@@ -203,12 +203,12 @@ rule pe_map_genome_star:
             "map_genome",
             "{sample}.pe.Log.final.out")
 
-    shadow: "full"
+    shadow: "minimal"
 
     params:
         sample_id = "{sample}",
         index = lambda wildcards:
-            os.path.join(
+            os.path.abspath(os.path.join(
                 config["star_indexes"],
                 get_sample(
                     'organism',
@@ -218,7 +218,7 @@ rule pe_map_genome_star:
                     'index_size',
                     search_id='index',
                     search_value=wildcards.sample),
-                "STAR_index"),
+                "STAR_index")),
         outFileNamePrefix = os.path.join(
             config["output_dir"],
             "samples",
@@ -339,7 +339,7 @@ rule pe_quantification_salmon:
             "libParams",
             "flenDist.txt")
 
-    shadow: "full"
+    shadow: "minimal"
 
     params:
         output_dir = os.path.join(
@@ -423,7 +423,7 @@ rule pe_genome_quantification_kallisto:
             "quant_kallisto",
             "abundance.h5")
 
-    shadow: "full"
+    shadow: "minimal"
 
     params:
         output_dir = os.path.join(
@@ -454,6 +454,7 @@ rule pe_genome_quantification_kallisto:
         -i {input.index} \
         -o {params.output_dir} \
         --pseudobam \
+        -t {threads} \
         {params.directionality}-stranded \
         {input.reads1} {input.reads2} > {output.pseudoalignment}) \
         2> {log.stderr}"

workflow/rules/single_end.snakefile.smk

@@ -151,16 +151,16 @@ rule map_genome_star:
             "map_genome",
             "{sample}.se.Log.final.out")
 
-    shadow: "full"
+    shadow: "minimal"
 
     params:
         sample_id = "{sample}",
         index = lambda wildcards:
-            os.path.join(
+            os.path.abspath(os.path.join(
                 config["star_indexes"],
                 get_sample('organism', search_id='index', search_value=wildcards.sample),
                 get_sample('index_size', search_id='index', search_value=wildcards.sample),
-                "STAR_index"),
+                "STAR_index")),
         outFileNamePrefix = os.path.join(
             config["output_dir"],
             "samples",
@@ -276,7 +276,7 @@ rule quantification_salmon:
             "libParams",
             "flenDist.txt")
 
-    shadow: "full"
+    shadow: "minimal"
 
     params:
         output_dir = os.path.join(
@@ -365,8 +365,7 @@ rule genome_quantification_kallisto:
             "quant_kallisto",
             "abundance.h5")
 
-
-    shadow: "full"
+    shadow: "minimal"
 
     params:
         output_dir = os.path.join(
@@ -410,6 +409,7 @@ rule genome_quantification_kallisto:
         -l {params.fraglen} \
         -s {params.fragsd} \
         --pseudobam \
+        -t {threads} \
         {params.directionality}-stranded \
         {input.reads} > {output.pseudoalignment};) \
         2> {log.stderr}"