.. |PipeCraft2_logo| image:: _static/PipeCraft2_icon_v2.png
  :width: 50
  :target: https://github.com/pipecraft2/pipecraft

.. raw:: html

    <style> .red {color:#ff0000; font-weight:bold; font-size:16px} </style>

.. role:: red


.. _dockerimages:

===============================
Docker images |PipeCraft2_logo|
===============================

Docker images (with the bioinformatic tools) used in PipeCraft2 are stored on `Dockerhub <https://hub.docker.com/u/pipecraft>`_. 
These images can be used to launch any tool with the Docker CLI to utilize the compiled tools.


Images used in PipeCraft2 v1.2.0
--------------------------------

+--------------------------------------+------------------------------------------------------------+--------------------------------+
| Image                                | Software                                                   | Used in ...                    |
+======================================+============================================================+================================+
|| pipecraft/vsearch_dada2:4-pc1.2.0   || vsearch v2.30.4, DADA 1.41, (Bioconductor 3.24, R v4.6.0) || DADA2, UNOISE & vsearch       |
||                                     || LULU v0.1.0, ORFfinder v0.4.3, seqkit v2.13.0, BLAST+     || pipelines, chimera filtering, |
||                                     ||                                                           || clustering, SINTAX,           |
||                                     ||                                                           || many QuickTools steps         |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/funbaront:1-pc1.2.0       || minimap2, samtools, bcftools, racon, medaka,              || FunBarONT pipeline            |
||                                     || vsearch v2.30.4, nanoplot, chopper, filtlong,             ||                               |
||                                     || ITSx, HMMER, BLAST, seqkit v2.13.0, nextflow,             ||                               |
||                                     || Python 3.10.14                                            ||                               |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/nextits:1.1.0-pc1.2.0     || NextITS v1.1.0 (extends vmikk/nextits:1.1.0),             || NextITS pipeline              |
||                                     || Nextflow v25.10.4                                         ||                               |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/optimotu:5.1-pc1.2.0      || optimotu_targets v5.1.0                                   || OptimOTU pipeline             |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/swarm:3.1                 || swarm v3.1.6, vsearch v2.30.4, seqkit v2.12.0,            || SWARM clustering              |
||                                     || parallel v20260122, numpy, polars                         ||                               |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/metamate:0.5.6-pc1.2.0    || metaMATE v0.5.6, BBMap v39.06, seqkit v2.8.1,             || metaMATE                      |
||                                     || mafft, R                                                  ||                               |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/metaworks:1.12.0-pc1.2.0  || MetaWorks v1.12.0, ORFfinder, seqkit v2.13.0, R           || MetaWorks (postprocessing)    |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/blast:2.16-pc1.2.0        || BLAST 2.16.0+, biopython, psutil v7.0.0,                  || BLAST taxonomy, BlasCh        |
||                                     || seqkit v2.13.0, gawk                                      ||                               |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/boldigger3:2.2.0          || BOLDigger3 v2.2.0, Python 3.12                            || QuickTools: BOLDigger3        |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/itsx:1.1.3-pc1.2.0        || ITSx v1.1.3, ITSx_HMMs profiles 2024.04.05,               || ITSx (QuickTools and          |
||                                     || HMMER v3.4, mothur v1.46.1, seqkit v2.13.0,               || pipelines)                    |
||                                     || biopython                                                 ||                               |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/cutadapt:5.2-pc1.2.0      || cutadapt v5.2, seqkit v2.13.0, biopython                  || Cut primers                   |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/trimmomatic:0.40-pc1.2.0  || Trimmomatic v0.40, seqkit v2.13.0                         || Quality filtering             |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/fastp:0.23.2-pc1.2.0      || fastp v0.23.2, seqkit v2.13.0                             || Quality filtering             |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/reorient:1-pc1.2.0        || fqgrep v0.4.4, seqkit v2.13.0                             || Reorient sequences            |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
|| pipecraft/deicode:0.2.4-pc1.2.0     || DEICODE v0.2.4, qiime2 2022.8                             || DEICODE (postprocessing)      |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
| ewels/multiqc:1.10                   | MultiQC v1.10                                              | Quality check                  |
+--------------------------------------+------------------------------------------------------------+--------------------------------+
| staphb/fastqc:0.11.9                 | FastQC v0.11.9                                             | Quality check                  |
+--------------------------------------+------------------------------------------------------------+--------------------------------+

Images used in PipeCraft2 v1.1.0
--------------------------------

+------------------------------+--------------------------------------+-----------------------------+
| Image                        | Software                             | Used in ...                 |
+==============================+======================================+=============================+
|| pipecraft/vsearch_dada2:3   || vsearch v2.29.4, dada2 v1.34,       || DADA2 pipeline,            |
||                             || ORFfinder v0.4.3 R v4.4.1,          || UNOISE & vsearch pipeline, |
||                             || seqkit v2.9.0, lulu v0.1.0          || LULU post-clustering       |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/vsearch_dada2_m:3 || For Mac M chips, vsearch v2.29.4, , || DADA2 pipeline (Mac),      |
||                             || dada2 v1.34, seqkit v2.9.0          || UNOISE & vsearch pipeline  |
||                             || lulu v0.1.0, ORFfinder v0.4.3,      || LULU post-clustering (Mac) |
||                             || R v4.4.1                            ||                            |
+------------------------------+--------------------------------------+-----------------------------+
| ewels/multiqc:1.10           | mutliqc v1.10                        | Quality check               |
+------------------------------+--------------------------------------+-----------------------------+
| staphb/fastqc:0.11.9         | fastqc v0.11.9                       | Quality check               |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/cutadapt:4.4      || cutadapt v4.4, seqkit v2.3.0,       || Cut primers                |
||                             || biopython v1.81, python3.10.12      ||                            |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/reorient:1         | fqgrep v0.4.4, seqkit v2.3.0         | Reorient sequences          |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/trimmomatic:0.39   | trimmomatic v0.39, seqkit v2.3.0     | Quality filtering           |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/itsx:1.1.3        || ITSx v1.1.3, seqkit v2.3.0,         || ITSx                       |
||                             || mothur v1.46.1                      ||                            |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/deicode:0.2.4      | DEICODE v0.2.4, qiime2-2002.2        | DEICODE                     |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/fastp:0.23.2       | fastp v0.23.2                        | Quality filtering           |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/blast:2.14        || BLAST 2.14.0+, biopython v1.81,     || BLAST                      |
||                             || gawk v5.1.0, python3.10.12          ||                            |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/metamate:1        || metamate v0.4.0, seqkit v2.8.1,     || metaMATE                   |
||                             || python3.10.13, biopython v1.83      ||                            |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/metaworks:1.12.0  || metaworks v1.12.0, seqkit v2.3.0,   ||                            |
||                             || R v4.1.2, ORFfinder v0.4.3          ||                            |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/optimotu:5        || optimotu v0.9.3,                    || OptimOTU pipeline          |
||                             || optimotu.pipeline v0.5.2,           ||                            |
||                             || optimotu_targets v5.0.0, R v4.3,    ||                            |
||                             || dada2 v1.30, cutadapt v5.0,         ||                            |
||                             || vsearch v2.30.0                     ||                            |
+------------------------------+--------------------------------------+-----------------------------+
|| vmikk/nextits:0.5.0         || nextITS v0.5.0,                     || NextITS pipeline           |
||                             || vsearch v2.22.1,                    ||                            |
||                             || cutadapt v4.3,                      ||                            |
||                             || itsx v1.1.3,                        ||                            |
||                             || blast v2.13,                        ||                            |
||                             || seqkit v2.4.0,                      ||                            |
||                             || fastp v0.23.2                       ||                            |
+------------------------------+--------------------------------------+-----------------------------+

Images used in PipeCraft2 v1.0.0
--------------------------------

+------------------------------+--------------------------------------+-----------------------------+
| Image                        | Software                             | Used in ...                 |
+==============================+======================================+=============================+
|| pipecraft/vsearch_dada2:2   || vsearch v2.23.0, dada2 v1.27,       || DADA2 pipeline,            |
||                             || ORFfinder v0.4.3 R v4.4.1,          || UNOISE & vsearch pipeline, |
||                             || seqkit v2.9.0, lulu v0.1.0          || LULU post-clustering       |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/cutadapt:3.5      || cutadapt v3.5, seqkit v2.3.0,       || Cut primers                |
||                             || biopython v1.80, python3.10.6       ||                            |
+------------------------------+--------------------------------------+-----------------------------+
| ewels/multiqc:1.10           | mutliqc v1.10                        | Quality check               |
+------------------------------+--------------------------------------+-----------------------------+
| staphb/fastqc:0.11.9         | fastqc v0.11.9                       | Quality check               |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/reorient:1         | fqgrep v0.4.4, seqkit v2.3.0         | Reorient sequences          |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/trimmomatic:0.39   | trimmomatic v0.39, seqkit v2.3.0     | Quality filtering           |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/itsx:1.1.3        || ITSx v1.1.3, seqkit v2.3.0,         || ITSx                       |
||                             || mothur v1.46.1                      ||                            |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/deicode:0.2.4      | DEICODE v0.2.4, qiime2-2002.2        | DEICODE                     |
+------------------------------+--------------------------------------+-----------------------------+
| pipecraft/fastp:0.23.2       | fastp v0.23.2                        | Quality filtering           |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/blast:2.14        || BLAST 2.14.0+, biopython v1.81,     || BLAST                      |
||                             || gawk v5.1.0, python3.10.12          ||                            |
+------------------------------+--------------------------------------+-----------------------------+
|| pipecraft/metaworks:1.12.0  || metaworks v1.12.0, seqkit v2.3.0,   ||                            |
||                             || R v4.1.2, ORFfinder v0.4.3          ||                            |
+------------------------------+--------------------------------------+-----------------------------+
|| vmikk/nextits:0.5.0         || nextITS v0.5.0,                     || NextITS pipeline           |
||                             || vsearch v2.22.1,                    ||                            |
||                             || cutadapt v4.3,                      ||                            |
||                             || itsx v1.1.3,                        ||                            |
||                             || blast v2.13,                        ||                            |
||                             || seqkit v2.4.0,                      ||                            |
||                             || fastp v0.23.2                       ||                            |
+------------------------------+--------------------------------------+-----------------------------+

Older images (used in PipeCraft2 vesions 0.1.X)
-----------------------------------------------

+-----------------------------+------------------------------------+
|| pipecraft/dada2:1.20       || vsearch v2.23,                    |
||                            || dada2 v1.20,                      |
||                            || seqkit v2.3.0                     |
+-----------------------------+------------------------------------+
|| pipecraft/vsearch:2.18     || vsearch v2.18,                    |
||                            || seqkit v2.3.0,                    |
||                            || python3.10.6,                     |
||                            || biopython v1.80                   |
+-----------------------------+------------------------------------+
|| pipecraft/metaworks:1.11.2 || metaworks v1.11.2,                |
||                            || seqkit v2.3.0,                    |
||                            || R v4.1.2,                         |
||                            || ORFfinder v0.4.3                  |
+-----------------------------+------------------------------------+
|| pipecraft/blast:2.12       || blast v2.12,                      |
||                            || biopython v1.80,                  |
||                            || gawk v5.1.0,                      |
||                            || python3.10.6                      |
+-----------------------------+------------------------------------+