Commit 7e471414 authored by peguerin's avatar peguerin
Browse files

readme update

parent 05c7fbef
......@@ -152,7 +152,7 @@ parameters | descriptions | softwares | rules | default values
container | absolute path of singularity container file `obitools.simg` | [singularity](https://singularity.lbl.gov/) | every rules need this container to work | /workdir/obitools.simg | absolute path of `simg` file
fastqFolderPath | absolute path of a folder which contains pairend-end raw reads `.fastq.gz` files and the sample description `.dat` files. | [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend), [ngsfilter](https://pythonhosted.org/OBITools/scripts/ngsfilter.html) | illuminapairedend, assign_sequences | /workdir/edna_miseq_rawdata/ | absolute path of a folder
fastqFiles | list of wildcard `{run}` where `{run}` is the name of the sequencing run | [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend) | illuminapairedend | seqrunA, seqrunB | list of strings
barcodeFiles | a dictionary with `{run}` as key and associated sample description file as value | ngsfilter | assign_sequences | {seqrunA : sample_description1.dat, seqrunB : sample_description2.dat} | dictionary
barcodeFiles | a dictionary with `{run}` as key and associated sample description file as value | [ngsfilter](https://pythonhosted.org/OBITools/scripts/ngsfilter.html) | assign_sequences | {seqrunA : sample_description1.dat, seqrunB : sample_description2.dat} | dictionary
s_min | score for keeping alignment. If the alignment score is below this threshold both the sequences are just concatenated. The mode attribute is set to the value joined | [illuminapairedend](https://pythonhosted.org/OBITools/scripts/illuminapairedend.html?highlight=illumina#module-illuminapairedend) | illuminapairedend | 40 | integer
count | minimum number of copy for keeping a sequence | [obigrep](https://pythonhosted.org/OBITools/scripts/obigrep.html?highlight=obigrep#module-obigrep) | good_length_samples | 10 | integer
seq_length | minimum length for keeping a sequence | [obigrep](https://pythonhosted.org/OBITools/scripts/obigrep.html?highlight=obigrep#module-obigrep) | good_length_samples | 20 | integer
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment