Commit e5443659 authored by peguerin's avatar peguerin
Browse files

singularityt in snakemake

parent 9bc0b19f

config.yaml

+11 −11
Original line number Diff line number Diff line
@@ -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

+8 −0
Original line number Diff line number Diff line
@@ -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: