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Merge pull request #27 from B-UMMI/fix_gap_plot
[Patch fix] - Gap and SPN plots
2 parents 7d2aba7 + 2ab52d1 commit d4ad75f

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‎README.md

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@@ -118,10 +118,6 @@ To use LMAS the following options are available:
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--abyssBloomSize Bloom filter size for the ABySS assembler.
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It must be a sting with a value and an unit.
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(default: 2G)
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--bcalm Boolean controling the execution of the BCALM2 assembler.
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(default: true)
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--bcalmKmerSize K-mer size for the BCALM2 assembler, as an intiger.
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(default 31)
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--gatb_minia Boolean controling the execution of the GATB Minia Pipeline assembler.
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(default: true)
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--gatbKmerSize K-mer sizes for the GATB Minia Pipeline assembler.

‎docs/dev/add_process.rst

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@@ -12,7 +12,6 @@ The `assembly.nf <https://github.com/B-UMMI/LMAS/tree/main/modules/assembly/asse
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The current available assemblers are:
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* `ABySS <https://github.com/bcgsc/abyss>`_
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* `BCALM 2 <https://github.com/GATB/bcalm>`_
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* `GATB-Minia Pipeline <https://github.com/GATB/gatb-minia-pipeline>`_
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* `IDBA <https://github.com/loneknightpy/idba>`_
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* `MEGAHIT <https://github.com/voutcn/megahit>`_
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.. code-block:: bash
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all_assemblies = ABYSS.out.assembly | mix(BCALM2.out.assembly,
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GATBMINIAPIPELINE.out.assembly,
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all_assemblies = ABYSS.out.assembly | mix(GATBMINIAPIPELINE.out.assembly,
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IDBA.out.assembly,
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MEGAHIT.out.assembly,
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METAHIPMER2.out.assembly,
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.. code-block:: bash
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all_versions = ABYSS.out.version | mix(BCALM2.out.version,
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GATBMINIAPIPELINE.out.version,
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all_versions = ABYSS.out.version | mix(GATBMINIAPIPELINE.out.version,
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IDBA.out.version,
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MEGAHIT.out.version,
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METAHIPMER2.out.version,

‎docs/getting_started/installation.rst

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@@ -146,10 +146,6 @@ To use LMAS the following options are available:
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--abyssBloomSize Bloom filter size for the ABySS assembler.
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It must be a sting with a value and an unit.
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(default: 2G)
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--bcalm Boolean controling the execution of the BCALM2 assembler.
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(default: true)
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--bcalmKmerSize K-mer size for the BCALM2 assembler, as an intiger.
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(default 31)
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--gatb_minia Boolean controling the execution of the GATB Minia Pipeline assembler.
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(default: true)
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--gatbKmerSize K-mer sizes for the GATB Minia Pipeline assembler.

‎docs/user/assemblers.rst

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@@ -35,18 +35,6 @@ graph, reducing memory requirements for de novo assembly. **It's a traditional s
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* **Date of last release:** 22/04/2021
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* **Container:** `cimendes/abyss:2.3.1-1 <https://hub.docker.com/repository/docker/cimendes/abyss>`_
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BCALM2
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^^^^^^
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This assembler, published by `Chikhi et al, 2016 <https://academic.oup.com/bioinformatics/article/32/12/i201/2289008>`_ in
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*Bioinformatics*, is a fast and low memory algorithm for graph compaction, consisting of three stages: careful distribution
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of input k-mers into buckets, parallel compaction of the buckets, and a parallel reunification step to glue together
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the compacted strings into unitigs. **It's a traditional single k-mer value De Bruijn assembler.**
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* **Source code:** https://github.com/GATB/bcalm
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* **Date of last release:** 22/05/2020
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* **Container:** `cimendes/bcalm:2.2.3-1 <https://hub.docker.com/repository/docker/cimendes/bcalm>`_
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GATB-Minia Pipeline
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^^^^^^^^^^^^^^^^^^^
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‎docs/user/basic_usage.rst

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--abyssBloomSize Bloom filter size for the ABySS assembler.
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It must be a sting with a value and an unit.
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(default: 2G)
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--bcalm Boolean controling the execution of the BCALM2 assembler.
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(default: true)
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--bcalmKmerSize K-mer size for the BCALM2 assembler, as an intiger.
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(default 31)
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--gatb_minia Boolean controling the execution of the GATB Minia Pipeline assembler.
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(default: true)
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--gatbKmerSize K-mer sizes for the GATB Minia Pipeline assembler.

‎docs/user/parameters.rst

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* **Default:** 2G
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BCALM2
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^^^^^^
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* **Param:** :code:`--bcalm`
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* **Definition:** Boolean controling the execution of the BCALM2 assembler.
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* **Default:** true
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----------------
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* **Param:** :code:`--bcalmKmerSize`
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* **Definition:** K-mer size for the BCALM2 assembler, as an intiger.
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* **Default:** 31
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GATB Minia Pipeline
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^^^^^^^^^^^^^^^^^^^
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‎modules/assembly/README.md

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@@ -5,9 +5,7 @@ This module contains the following processes:
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- REFORMAT
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- merges the paired-end read files with [BBtools reformat.sh](https://sourceforge.net/projects/bbmap/)
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- ABYSS
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- Assemble the input fastq data with [ABySS](https://github.com/bcgsc/abyss) assembler. Returns it's assembly and the software version.
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- BCALM2
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- Assemble the input fastq data with [BCALM 2](https://github.com/GATB/bcalm) assembler. Returns it's assembly and the software version.
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- Assemble the input fastq data with [ABySS](https://github.com/bcgsc/abyss) assembler. Returns it's assembly and the software version.
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- GATBMINIAPIPELINE
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- Assemble the input fastq data with [GATB-Minia Pipeline](https://github.com/GATB/gatb-minia-pipeline) assembler. Returns it's assembly and the software version.
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- IDBA

‎modules/postprocessing/postprocessing.nf

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PROCESS_SHRIMP_PLOT(phred_csv)
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PLOT_CONTIG_DISTRIBUTION(mapping_df_csv)
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GAP_ASSESSMENT(paf, triple_reference)
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PLOT_GAP_BOXPLOT(GAP_ASSESSMENT.out.json)
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PLOT_GAP_REFERENCE(GAP_ASSESSMENT.out.csv)
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PLOT_GAP_BOXPLOT(GAP_ASSESSMENT.out.json | collect)
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PLOT_GAP_REFERENCE(GAP_ASSESSMENT.out.csv | collect)
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SNP_ASSESSMENT(paf, triple_reference)
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PLOT_SNP_REFERENCE(SNP_ASSESSMENT.out.csv)
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PLOT_SNP_REFERENCE(SNP_ASSESSMENT.out.csv | collect)
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MISASSEMBLY(paf)
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PROCESS_MISASSEMBLY(MISASSEMBLY.out.trace_pkl | collect, MISASSEMBLY.out.contig_length_pkl | collect, MISASSEMBLY.out.misassembly_json | collect, MISASSEMBLY.out.misassembled_reference_json | collect)
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PLOT_MISASSEMBLY(MISASSEMBLY.out.csv | collect)

‎templates/process_assembly_stats_global.py

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ASSEMBLY_STATS_GLOBAL_FILE = '$assembly_stats_global_files'.split()
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ASSEMBLY_STATS_GLOBAL_FILE_JSON = "$json_report".split()
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N_TARGET = float("$params.n_target")
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ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "BCALM2": json.loads("$params.bcalm"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"),
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ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"),
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"MetaHipMer2": json.loads("$params.metahipmer2"), "MINIA": json.loads("$params.minia"), "MEGAHIT": json.loads("$params.megahit"),
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"metaSPAdes": json.loads("$params.metaspades"), "Unicycler": json.loads("$params.unicycler"), "SPAdes": json.loads("$params.spades"),
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"SKESA": json.loads("$params.skesa"), "VelvetOptimiser": json.loads("$params.velvetoptimiser"), "IDBA-UD": json.loads("$params.idba")}

‎templates/process_assembly_stats_mapping.py

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if __file__.endswith(".command.sh"):
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ASSEMBLY_STATS_GLOBAL_FILE_JSON = "$json_report".split()
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ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "BCALM2": json.loads("$params.bcalm"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"),
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ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"),
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"MetaHipMer2": json.loads("$params.metahipmer2"), "MINIA": json.loads("$params.minia"), "MEGAHIT": json.loads("$params.megahit"),
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"metaSPAdes": json.loads("$params.metaspades"), "Unicycler": json.loads("$params.unicycler"), "SPAdes": json.loads("$params.spades"),
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"SKESA": json.loads("$params.skesa"), "VelvetOptimiser": json.loads("$params.velvetoptimiser"), "IDBA-UD": json.loads("$params.idba")}

‎templates/process_versions.py

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ASSEMBLER_PROCESS_DICT = {
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"ABySS": "ABYSS",
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"BCALM2": "BCALM2",
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"GATBMiniaPipeline": "GATBMINIAPIPELINE",
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"MetaHipMer2": "METAHIPMER2",
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"MINIA": "MINIA",

‎templates/utils.py

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COLOURS = ['#a6cee3', '#1f78b4', '#b2df8a', '#33a02c', '#fb9a99', '#e31a1c',
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'#fdbf6f', '#ff7f00', '#cab2d6', '#6a3d9a', '#ebdb75', '#b15928']
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ASSEMBLER_NAMES = ["ABySS", "BCALM2", "GATBMiniaPipeline", "MetaHipMer2", "MINIA", "MEGAHIT", "metaSPAdes", "Unicycler", "SPAdes",
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ASSEMBLER_NAMES = ["ABySS", "GATBMiniaPipeline", "MetaHipMer2", "MINIA", "MEGAHIT", "metaSPAdes", "Unicycler", "SPAdes",
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"SKESA", "VelvetOptimiser", "IDBA-UD"]
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ASSEMBLER_PROCESS_LIST = ["ABYSS", "BCALM2", "GATBMINIAPIPELINE", "MINIA", "METAHIPMER2", "MEGAHIT", "METASPADES", "UNICYCLER", "SPADES",
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ASSEMBLER_PROCESS_LIST = ["ABYSS", "GATBMINIAPIPELINE", "MINIA", "METAHIPMER2", "MEGAHIT", "METASPADES", "UNICYCLER", "SPADES",
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"SKESA", "VELVETOPTIMISER", "IDBA"]
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