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Commit 9ec30196 authored by ahb-ufz's avatar ahb-ufz
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adapters paired trimming

parent 10886ebb
Pipeline #39846 failed with stages
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              Showing with 7 additions and 5 deletions
              config/config.imp.yaml
              View file @ 9ec30196
              ...@@ -44,7 +44,7 @@ trimmomatic: ...@@ -44,7 +44,7 @@ trimmomatic:
              target_length: 40 target_length: 40
              nextseq: false nextseq: false
              filtering: filtering:
              filter: hg38 filter: "phiX174 hg38"
              sortmerna: sortmerna:
              files: files:
              - rfam-5.8s-database-id98 - rfam-5.8s-database-id98
              ......
              workflow/rules/Preprocessing/trimming.smk
              View file @ 9ec30196
              ...@@ -12,14 +12,15 @@ if config['nextseq']: ...@@ -12,14 +12,15 @@ if config['nextseq']:
              threads: 10 threads: 10
              params: params:
              runtime="12:00:00", runtime="12:00:00",
              mem = MEMCORE mem = MEMCORE,
              adapter = lambda wildcards: config["trimmomatic"]["adapter"][wildcards.type]
              conda: ENVDIR + "/IMP_preprocessing.yaml" conda: ENVDIR + "/IMP_preprocessing.yaml"
              log: "logs/preprocessing_trimming.{type}.log" log: "logs/preprocessing_trimming.{type}.log"
              message: "trimming: Trimmming {wildcards.type} reads." message: "trimming: Trimmming {wildcards.type} reads."
              shell: shell:
              """ """
              trimmomatic PE -threads {threads} {input[0]} {input[1]} {output} \ trimmomatic PE -threads {threads} {input[0]} {input[1]} {output} \
              ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \ ILLUMINACLIP:{DBPATH}/adapters/{params.adapter}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
              LEADING:{config[trimmomatic][leading]} \ LEADING:{config[trimmomatic][leading]} \
              TRAILING:{config[trimmomatic][trailing]} \ TRAILING:{config[trimmomatic][trailing]} \
              SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \ SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \
              ...@@ -118,14 +119,15 @@ else: ...@@ -118,14 +119,15 @@ else:
              threads: 10 threads: 10
              params: params:
              runtime="12:00:00", runtime="12:00:00",
              mem = MEMCORE mem = MEMCORE,
              adapter = lambda wildcards: config["trimmomatic"]["adapter"][wildcards.type]
              conda: ENVDIR + "/IMP_preprocessing.yaml" conda: ENVDIR + "/IMP_preprocessing.yaml"
              log: "logs/preprocessing_trimming.{type}.log" log: "logs/preprocessing_trimming.{type}.log"
              message: "trimming: Trimmming {wildcards.type} reads." message: "trimming: Trimmming {wildcards.type} reads."
              shell: shell:
              """ """
              trimmomatic PE -threads {threads} {input[0]} {input[1]} {output} \ trimmomatic PE -threads {threads} {input[0]} {input[1]} {output} \
              ILLUMINACLIP:{DBPATH}/adapters/{config[trimmomatic][adapter]}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \ ILLUMINACLIP:{DBPATH}/adapters/{params.adapter}.fa:{config[trimmomatic][seed_mismatch]}:{config[trimmomatic][palindrome_clip_threshold]}:{config[trimmomatic][simple_clip_threshold]} \
              LEADING:{config[trimmomatic][leading]} \ LEADING:{config[trimmomatic][leading]} \
              TRAILING:{config[trimmomatic][trailing]} \ TRAILING:{config[trimmomatic][trailing]} \
              SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \ SLIDINGWINDOW:{config[trimmomatic][window_size]}:{config[trimmomatic][window_quality]} \
              ......
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