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Commit 57b33a92 authored by seehagec01's avatar seehagec01
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setup

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---
index: "results/reference/index"
samples: "resources/samples.tsv"
bowtieparams: "-q"
# schöner wäre sowas:
bowtie:
N: 0 # Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
L: 22 # Sets the length of the seed substrings to align during multiseed alignment.
extra: "--ignore-quals --end-to-end" # users can put here all other parameters or simply leave empty
File added
IndentationError in line 6 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 6)
File "/Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/Snakefile", line 11, in <module>
File "/opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/tokenize.py", line 514, in _tokenize
IndentationError in line 6 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 6)
File "/Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/Snakefile", line 11, in <module>
File "/opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/tokenize.py", line 514, in _tokenize
IndentationError in line 6 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 6)
File "/Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/Snakefile", line 11, in <module>
File "/opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/tokenize.py", line 514, in _tokenize
IndentationError in line 6 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 6)
File "/Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/Snakefile", line 11, in <module>
File "/opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/tokenize.py", line 514, in _tokenize
IndentationError in line 6 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 6)
File "/Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/Snakefile", line 10, in <module>
File "/opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/tokenize.py", line 514, in _tokenize
IndentationError in line 6 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 6)
File "/Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/Snakefile", line 11, in <module>
File "/opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/tokenize.py", line 514, in _tokenize
IndentationError in line 6 of <tokenize>:
unindent does not match any outer indentation level (<tokenize>, line 6)
File "/Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/Snakefile", line 11, in <module>
File "/opt/homebrew/Cellar/python@3.10/3.10.2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/tokenize.py", line 514, in _tokenize
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024604_tiny.sam
wildcards: sample=ERR024604_tiny
affected files:
results/fastq/ERR024604_tiny.fastq.gz
Building DAG of jobs...
WildcardError in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Wildcards in input files cannot be determined from output files:
'number'
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024608_tiny.sam
wildcards: sample=ERR024608_tiny
affected files:
results/fastq/ERR024608_tiny_1.fastq.gzresults/fastq/ERR024608_tiny_2.fastq.gz
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024608_tiny.sam
wildcards: sample=ERR024608_tiny
affected files:
results/fastq/ERR024608_tiny_1.fastq.gzresults/fastq/ERR024608_tiny_2.fastq.gz
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024604_tiny.sam
wildcards: sample=ERR024604_tiny
affected files:
results/fastq/ERR024604_tiny_1.fastq.gzresults/fastq/ERR024604_tiny_2.fastq.gz
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024606_tiny.sam
wildcards: sample=ERR024606_tiny
affected files:
results/fastq/ERR024606_tiny_1.fastq.gzresults/fastq/ERR024606_tiny_2.fastq.gz
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024605_tiny.sam
wildcards: sample=ERR024605_tiny
affected files:
results/fastq/ERR024605_tiny_1.fastq.gzresults/fastq/ERR024605_tiny_2.fastq.gz
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024608_tiny.sam
wildcards: sample=ERR024608_tiny
affected files:
results/fastq/ERR024608_tiny_1.fastq.gzresults/fastq/ERR024608_tiny_2.fastq.gz
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024606_tiny.sam
wildcards: sample=ERR024606_tiny
affected files:
results/fastq/ERR024606_tiny_2.fastq.gz
results/fastq/ERR024606_tiny_1.fastq.gz
Building DAG of jobs...
MissingInputException in line 1 of /Users/charlotteseehagen/Documents/Uni/swp-workflows/workflow/rules/bowtie.smk:
Missing input files for rule map:
output: results/sam/ERR024605_tiny.sam
wildcards: sample=ERR024605_tiny
affected files:
results/fastq/ERR024605_tiny_2.fastq.gz
results/fastq/ERR024605_tiny_1.fastq.gz
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