singularityt in snakemake

config.yaml

@@ -15,17 +15,17 @@ fastqFiles:
   - 161124_SND393_A_L005_GWM-858
   - 161124_SND393_A_L005_GWM-859
 barcodeFiles:
-  - 161124_SND393_A_L005_GWM-849 : MB1016K_Teleo
-  - 161124_SND393_A_L005_GWM-850 : MB1016L_Teleo
-  - 161124_SND393_A_L005_GWM-851 : MB1016M_Teleo
-  - 161124_SND393_A_L005_GWM-852 : MB1016N_Teleo
-  - 161124_SND393_A_L005_GWM-853 : MB1016O_Teleo
-  - 161124_SND393_A_L005_GWM-854 : MB1016P_Teleo
-  - 161124_SND393_A_L005_GWM-855 : MB1016Q_Teleo
-  - 161124_SND393_A_L005_GWM-856 : MB1016R_Teleo
-  - 161124_SND393_A_L005_GWM-857 : MB1016S_Teleo
-  - 161124_SND393_A_L005_GWM-858 : MB1016T_Teleo
-  - 161124_SND393_A_L005_GWM-859 : MB1016U_Teleo
+  161124_SND393_A_L005_GWM-849 : MB1016K_Teleo
+  161124_SND393_A_L005_GWM-850 : MB1016L_Teleo
+  161124_SND393_A_L005_GWM-851 : MB1016M_Teleo
+  161124_SND393_A_L005_GWM-852 : MB1016N_Teleo
+  161124_SND393_A_L005_GWM-853 : MB1016O_Teleo
+  161124_SND393_A_L005_GWM-854 : MB1016P_Teleo
+  161124_SND393_A_L005_GWM-855 : MB1016Q_Teleo
+  161124_SND393_A_L005_GWM-856 : MB1016R_Teleo
+  161124_SND393_A_L005_GWM-857 : MB1016S_Teleo
+  161124_SND393_A_L005_GWM-858 : MB1016T_Teleo
+  161124_SND393_A_L005_GWM-859 : MB1016U_Teleo
 illuminapairedend:
   s_min : 40
 good_length_samples:

rules/step1.smk

@@ -9,6 +9,8 @@ rule illuminapairedend:
         R2='raw/{run}_R2.fastq.gz'
     output:
         fq='assembled/{run}/{run}.fastq'
+    singularity:
+        config["container"]
     log:
         'log/illuminapairedend/{run}.log'
     params:
@@ -22,6 +24,8 @@ rule remove_unaligned:
         fq='assembled/{run}/{run}.fastq'
     output:
         ali='assembled/{run}/{run}.ali.fastq'
+    singularity:
+        config["container"]
     log:
         'log/remove_unaligned/{run}.log'
     shell:
@@ -35,6 +39,8 @@ rule assign_sequences:
     output:
         assign='assembled/{run}/{run}.ali.assigned.fastq',
         unid='assembled/{run}/{run}.unidentified.fastq'
+    singularity:
+        config["container"]
     log:
         'log/assign_sequences/{run}.log'
     shell:
@@ -46,6 +52,8 @@ rule split_sequences:
         'assembled/{run}/{run}.ali.assigned.fastq'
     params:
         'samples/{run}_sample_'
+    singularity:
+        config["container"]
     log:
         'log/split_sequences/{run}.log'
     shell: