The bioBakery help forum

--run-trim-repetitive and --sequencer-source not part of Docker, Conda, or Pip

Dear Kneaddata Developers,

Thank you for such a great product. I have been following the tutorial from https://github.com/biobakery/kneaddata. I have tried using Docker, Conda, and Pip to download kneaddata, all had versions 0.7.10, but none of them have the --run-trim-repetitive or
–sequencer-source options mentioned in the tutorial, as seen below with the Conda version. Is this going to be added a an upcoming version of kneaddata, or am I missing something in my downloading process? Thank you for your time and help.

Sincerely,

David

(base) microbiology@Willow:~ kneaddata --version kneaddata v0.7.10 (base) microbiology@Willow:~ kneaddata --help
usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT_DIR
[-db REFERENCE_DB] [–bypass-trim]
[–output-prefix OUTPUT_PREFIX] [-t <1>] [-p <1>]
[-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf]
[–run-fastqc-start] [–run-fastqc-end] [–store-temp-output]
[–remove-intermediate-output] [–cat-final-output]
[–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG]
[–trimmomatic TRIMMOMATIC_PATH] [–max-memory MAX_MEMORY]
[–trimmomatic-options TRIMMOMATIC_OPTIONS]
[–sequencer-source {NexteraPE,TruSeq2,TruSeq3}]
[–bowtie2 BOWTIE2_PATH] [–bowtie2-options BOWTIE2_OPTIONS]
[–no-discordant] [–reorder] [–serial]
[–bmtagger BMTAGGER_PATH] [–trf TRF_PATH] [–match MATCH]
[–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI]
[–minscore MINSCORE] [–maxperiod MAXPERIOD]
[–fastqc FASTQC_PATH]

KneadData

optional arguments:
-h, --help show this help message and exit
-v, --verbose additional output is printed

global options:
–version show program’s version number and exit
-i INPUT, --input INPUT
input FASTQ file (add a second argument instance to run with paired input files)
-o OUTPUT_DIR, --output OUTPUT_DIR
directory to write output files
-db REFERENCE_DB, --reference-db REFERENCE_DB
location of reference database (additional arguments add databases)
–bypass-trim bypass the trim step
–output-prefix OUTPUT_PREFIX
prefix for all output files
[ DEFAULT : $SAMPLE_kneaddata ]
-t <1>, --threads <1>
number of threads
[ Default : 1 ]
-p <1>, --processes <1>
number of processes
[ Default : 1 ]
-q {phred33,phred64}, --quality-scores {phred33,phred64}
quality scores
[ DEFAULT : phred33 ]
–run-bmtagger run BMTagger instead of Bowtie2 to identify contaminant reads
–bypass-trf option to bypass the removal of tandem repeats
–run-fastqc-start run fastqc at the beginning of the workflow
–run-fastqc-end run fastqc at the end of the workflow
–store-temp-output store temp output files
[ DEFAULT : temp output files are removed ]
–remove-intermediate-output
remove intermediate output files
[ DEFAULT : intermediate output files are stored ]
–cat-final-output concatenate all final output files
[ DEFAULT : final output is not concatenated ]
–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
level of log messages
[ DEFAULT : DEBUG ]
–log LOG log file
[ DEFAULT : $OUTPUT_DIR/$SAMPLE_kneaddata.log ]

trimmomatic arguments:
–trimmomatic TRIMMOMATIC_PATH
path to trimmomatic
[ DEFAULT : $PATH ]
–max-memory MAX_MEMORY
max amount of memory
[ DEFAULT : 500m ]
–trimmomatic-options TRIMMOMATIC_OPTIONS
options for trimmomatic
[ DEFAULT : ILLUMINACLIP:/-SE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:50 ]
MINLEN is set to 50 percent of total input read length
–sequencer-source {NexteraPE,TruSeq2,TruSeq3}
options for sequencer-source
[ DEFAULT : NexteraPE]

bowtie2 arguments:
–bowtie2 BOWTIE2_PATH
path to bowtie2
[ DEFAULT : $PATH ]
–bowtie2-options BOWTIE2_OPTIONS
options for bowtie2
[ DEFAULT : --very-sensitive ]
–no-discordant do not include discordant alignments for pairs (ie one of the two pairs aligns)
[ DEFAULT : Discordant alignments are included ]
–reorder order the sequences in the same order as the input
[ DEFAULT : With discordant paired alignments sequences are not ordered ]
–serial filter the input in serial for multiple databases so a subset of reads are processed in each database search

bmtagger arguments:
–bmtagger BMTAGGER_PATH
path to BMTagger
[ DEFAULT : $PATH ]

trf arguments:
–trf TRF_PATH path to TRF
[ DEFAULT : $PATH ]
–match MATCH matching weight
[ DEFAULT : 2 ]
–mismatch MISMATCH mismatching penalty
[ DEFAULT : 7 ]
–delta DELTA indel penalty
[ DEFAULT : 7 ]
–pm PM match probability
[ DEFAULT : 80 ]
–pi PI indel probability
[ DEFAULT : 10 ]
–minscore MINSCORE minimum alignment score to report
[ DEFAULT : 50 ]
–maxperiod MAXPERIOD
maximum period size to report
[ DEFAULT : 500 ]

fastqc arguments:
–fastqc FASTQC_PATH path to fastqc
[ DEFAULT : $PATH ]

Oops, sorry missed that -sequencer-source was there.