rbartelme
commented
4 years ago added R libraries vegan, zetadiv, deblur to docker file as well.
Closed rbartelme closed 4 years ago
rbartelme
commented
4 years ago added R libraries vegan, zetadiv, deblur to docker file as well.
rbartelme
commented
4 years ago dada2 biocontainers base image does not support apt-get, so I'll switch to using the rocker Rstudio tidyverse base image. And fall deep into the C dependencies rabbit hole.
rbartelme
commented
4 years ago Having issues with R package versioning vs. Rlang vs. container OS.
rbartelme
commented
4 years ago deblur and decontam are not available for R 3.6.1
rbartelme
commented
4 years ago Switching base container to rocker/verse:4.0.0-ubuntu18.04
rbartelme
commented
4 years ago Need to troubleshoot cutadapt installs, apt install -y cutadapt gives version 1.19 not version 2.1.
Inside the Rstudio environment terminal version 1.9 does not respond to the --help flag properly, and throws an error.
I'll try installing pip3 and then using pip to install cutadapt...this should hopefully resolve the versioning and CLI.
I should also move the R installs above this in the Dockerfile to speed up the cached installs while experimenting with the ideal cutadapt install.
rbartelme
commented
4 years ago Help works with cutadapt, but is still deprecated version (without multithreading/compression).
cutadapt version 1.15
Copyright (C) 2010-2017 Marcel Martin <marcel.martin@scilifelab.se>
cutadapt removes adapter sequences from high-throughput sequencing reads.
Usage:
cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq
For paired-end reads:
cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq
Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard
characters are supported. The reverse complement is *not* automatically
searched. All reads from input.fastq will be written to output.fastq with the
adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter
sequences can be given (use further -a options), but only the best-matching
adapter will be removed.
Input may also be in FASTA format. Compressed input and output is supported and
auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for
standard input/output. Without the -o option, output is sent to standard output.
Citation:
Marcel Martin. Cutadapt removes adapter sequences from high-throughput
sequencing reads. EMBnet.Journal, 17(1):10-12, May 2011.
http://dx.doi.org/10.14806/ej.17.1.200
Use "cutadapt --help" to see all command-line options.
See http://cutadapt.readthedocs.io/ for full documentation.
Options:
--version show program's version number and exit
-h, --help show this help message and exit
--debug Print debugging information.
-f FORMAT, --format=FORMAT
Input file format; can be either 'fasta', 'fastq' or
'sra-fastq'. Ignored when reading csfasta/qual files.
Default: auto-detect from file name extension.
-j CORES, --cores=CORES
Number of CPU cores to use. Default: 1
Finding adapters:
Parameters -a, -g, -b specify adapters to be removed from each read
(or from the first read in a pair if data is paired). If specified
multiple times, only the best matching adapter is trimmed (but see the
--times option). When the special notation 'file:FILE' is used,
adapter sequences are read from the given FASTA file.
-a ADAPTER, --adapter=ADAPTER
Sequence of an adapter ligated to the 3' end (paired
data: of the first read). The adapter and subsequent
bases are trimmed. If a '$' character is appended
('anchoring'), the adapter is only found if it is a
suffix of the read.
-g ADAPTER, --front=ADAPTER
Sequence of an adapter ligated to the 5' end (paired
data: of the first read). The adapter and any
preceding bases are trimmed. Partial matches at the 5'
end are allowed. If a '^' character is prepended
('anchoring'), the adapter is only found if it is a
prefix of the read.
-b ADAPTER, --anywhere=ADAPTER
Sequence of an adapter that may be ligated to the 5'
or 3' end (paired data: of the first read). Both types
of matches as described under -a und -g are allowed.
If the first base of the read is part of the match,
the behavior is as with -g, otherwise as with -a. This
option is mostly for rescuing failed library
preparations - do not use if you know which end your
adapter was ligated to!
-e ERROR_RATE, --error-rate=ERROR_RATE
Maximum allowed error rate (no. of errors divided by
the length of the matching region). Default: 0.1
--no-indels Allow only mismatches in alignments. Default: allow
both mismatches and indels
-n COUNT, --times=COUNT
Remove up to COUNT adapters from each read. Default: 1
-O MINLENGTH, --overlap=MINLENGTH
Require MINLENGTH overlap between read and adapter for
an adapter to be found. Default: 3
--match-read-wildcards
Interpret IUPAC wildcards in reads. Default: False
-N, --no-match-adapter-wildcards
Do not interpret IUPAC wildcards in adapters.
--no-trim Match and redirect reads to output/untrimmed-output as
usual, but do not remove adapters.
--mask-adapter Mask adapters with 'N' characters instead of trimming
them.
Additional read modifications:
-u LENGTH, --cut=LENGTH
Remove bases from each read (first read only if
paired). If LENGTH is positive, remove bases from the
beginning. If LENGTH is negative, remove bases from
the end. Can be used twice if LENGTHs have different
signs. This is applied *before* adapter trimming.
--nextseq-trim=3'CUTOFF
NextSeq-specific quality trimming (each read). Trims
also dark cycles appearing as high-quality G bases.
-q [5'CUTOFF,]3'CUTOFF, --quality-cutoff=[5'CUTOFF,]3'CUTOFF
Trim low-quality bases from 5' and/or 3' ends of each
read before adapter removal. Applied to both reads if
data is paired. If one value is given, only the 3' end
is trimmed. If two comma-separated cutoffs are given,
the 5' end is trimmed with the first cutoff, the 3'
end with the second.
--quality-base=QUALITY_BASE
Assume that quality values in FASTQ are encoded as
ascii(quality + QUALITY_BASE). This needs to be set to
64 for some old Illumina FASTQ files. Default: 33
-l LENGTH, --length=LENGTH
Shorten reads to LENGTH. This and the following
modifications are applied after adapter trimming.
--trim-n Trim N's on ends of reads.
--length-tag=TAG Search for TAG followed by a decimal number in the
description field of the read. Replace the decimal
number with the correct length of the trimmed read.
For example, use --length-tag 'length=' to correct
fields like 'length=123'.
--strip-suffix=STRIP_SUFFIX
Remove this suffix from read names if present. Can be
given multiple times.
-x PREFIX, --prefix=PREFIX
Add this prefix to read names. Use {name} to insert
the name of the matching adapter.
-y SUFFIX, --suffix=SUFFIX
Add this suffix to read names; can also include {name}
Filtering of processed reads:
Filters are applied after above read modifications. Paired-end reads
are always discarded pairwise (see also --pair-filter).
-m LENGTH, --minimum-length=LENGTH
Discard reads shorter than LENGTH. Default: 0
-M LENGTH, --maximum-length=LENGTH
Discard reads longer than LENGTH. Default: no limit
--max-n=COUNT Discard reads with more than COUNT 'N' bases. If COUNT
is a number between 0 and 1, it is interpreted as a
fraction of the read length.
--discard-trimmed, --discard
Discard reads that contain an adapter. Also use -O to
avoid discarding too many randomly matching reads!
--discard-untrimmed, --trimmed-only
Discard reads that do not contain an adapter.
Output:
--quiet Print only error messages.
-o FILE, --output=FILE
Write trimmed reads to FILE. FASTQ or FASTA format is
chosen depending on input. The summary report is sent
to standard output. Use '{name}' in FILE to
demultiplex reads into multiple files. Default: write
to standard output
--info-file=FILE Write information about each read and its adapter
matches into FILE. See the documentation for the file
format.
-r FILE, --rest-file=FILE
When the adapter matches in the middle of a read,
write the rest (after the adapter) to FILE.
--wildcard-file=FILE
When the adapter has N wildcard bases, write adapter
bases matching wildcard positions to FILE. (Inaccurate
with indels.)
--too-short-output=FILE
Write reads that are too short (according to length
specified by -m) to FILE. Default: discard reads
--too-long-output=FILE
Write reads that are too long (according to length
specified by -M) to FILE. Default: discard reads
--untrimmed-output=FILE
Write reads that do not contain any adapter to FILE.
Default: output to same file as trimmed reads
Colorspace options:
-c, --colorspace Enable colorspace mode
-d, --double-encode
Double-encode colors (map 0,1,2,3,4 to A,C,G,T,N).
-t, --trim-primer Trim primer base and the first color
--strip-f3 Strip the _F3 suffix of read names
--maq, --bwa MAQ- and BWA-compatible colorspace output. This
enables -c, -d, -t, --strip-f3 and -y '/1'.
-z, --zero-cap Change negative quality values to zero. Enabled by
default in colorspace mode since many tools have
problems with negative qualities
--no-zero-cap Disable zero capping
Paired-end options:
The -A/-G/-B/-U options work like their -a/-b/-g/-u counterparts, but
are applied to the second read in each pair.
-A ADAPTER 3' adapter to be removed from second read in a pair.
-G ADAPTER 5' adapter to be removed from second read in a pair.
-B ADAPTER 5'/3 adapter to be removed from second read in a pair.
-U LENGTH Remove LENGTH bases from second read in a pair (see
--cut).
-p FILE, --paired-output=FILE
Write second read in a pair to FILE.
--pair-filter=(any|both)
Which of the reads in a paired-end read have to match
the filtering criterion in order for the pair to be
filtered. Default: any
--interleaved Read and write interleaved paired-end reads.
--untrimmed-paired-output=FILE
Write second read in a pair to this FILE when no
adapter was found in the first read. Use this option
together with --untrimmed-output when trimming paired-
end reads. Default: output to same file as trimmed
reads
--too-short-paired-output=FILE
Write second read in a pair to this file if pair is
too short. Use together with --too-short-output.
--too-long-paired-output=FILE
Write second read in a pair to this file if pair is
too long. Use together with --too-long-output.```
Use Case: Container for processing amplicon data from raw paired illumina fastq format to merged/clustered amplicon data
Based on Mike Lee's workflow.