Commit e5443659 authored by peguerin's avatar peguerin

singularityt in snakemake

parent 9bc0b19f
......@@ -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:
......
......@@ -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:
......
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