Merge pull request #27 from B-UMMI/fix_gap_plot

[Patch fix] - Gap and SPN plots
B-UMMI · Jul 4, 2022 · d4ad75f · d4ad75f
2 parents 7d2aba7 + 2ab52d1
commit d4ad75f
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Showing 12 changed files with 10 additions and 58 deletions.
diff --git a/README.md b/README.md
@@ -118,10 +118,6 @@ To use LMAS the following options are available:
          --abyssBloomSize           Bloom filter size for the ABySS assembler.
                                     It must be a sting with a value and an unit.
                                     (default: 2G)
-         --bcalm                    Boolean controling the execution of the BCALM2 assembler.
-                                    (default: true)
-         --bcalmKmerSize            K-mer size for the BCALM2 assembler, as an intiger.
-                                    (default 31)
          --gatb_minia               Boolean controling the execution of the GATB Minia Pipeline assembler.
                                     (default: true)
          --gatbKmerSize             K-mer sizes for the GATB Minia Pipeline assembler.

diff --git a/docs/dev/add_process.rst b/docs/dev/add_process.rst
@@ -12,7 +12,6 @@ The `assembly.nf <https://github.com/B-UMMI/LMAS/tree/main/modules/assembly/asse
 The current available assemblers are:
 
 * `ABySS <https://github.com/bcgsc/abyss>`_
-* `BCALM 2 <https://github.com/GATB/bcalm>`_ 
 * `GATB-Minia Pipeline <https://github.com/GATB/gatb-minia-pipeline>`_
 * `IDBA <https://github.com/loneknightpy/idba>`_
 * `MEGAHIT <https://github.com/voutcn/megahit>`_
@@ -152,8 +151,7 @@ It should look like:
 
 .. code-block:: bash
 
-    all_assemblies = ABYSS.out.assembly | mix(BCALM2.out.assembly, 
-                                              GATBMINIAPIPELINE.out.assembly,
+    all_assemblies = ABYSS.out.assembly | mix(GATBMINIAPIPELINE.out.assembly,
                                               IDBA.out.assembly,
                                               MEGAHIT.out.assembly,
                                               METAHIPMER2.out.assembly,
@@ -175,8 +173,7 @@ It should look like:
 
 .. code-block:: bash
 
-    all_versions = ABYSS.out.version | mix(BCALM2.out.version, 
-                                           GATBMINIAPIPELINE.out.version,
+    all_versions = ABYSS.out.version | mix(GATBMINIAPIPELINE.out.version,
                                            IDBA.out.version,
                                            MEGAHIT.out.version,
                                            METAHIPMER2.out.version,

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

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

diff --git a/docs/user/basic_usage.rst b/docs/user/basic_usage.rst
@@ -105,10 +105,6 @@ To use LMAS the following options are available:
          --abyssBloomSize           Bloom filter size for the ABySS assembler.
                                     It must be a sting with a value and an unit.
                                     (default: 2G)
-         --bcalm                    Boolean controling the execution of the BCALM2 assembler.
-                                    (default: true)
-         --bcalmKmerSize            K-mer size for the BCALM2 assembler, as an intiger.
-                                    (default 31)
          --gatb_minia               Boolean controling the execution of the GATB Minia Pipeline assembler.
                                     (default: true)
          --gatbKmerSize             K-mer sizes for the GATB Minia Pipeline assembler.

diff --git a/docs/user/parameters.rst b/docs/user/parameters.rst
@@ -120,24 +120,6 @@ ABySS
 
 * **Default:** 2G
 
-BCALM2
-^^^^^^
-
-* **Param:** :code:`--bcalm`
-
-* **Definition:** Boolean controling the execution of the BCALM2 assembler.
-
-* **Default:** true
-
-----------------
-
-* **Param:** :code:`--bcalmKmerSize`
-
-* **Definition:** K-mer size for the BCALM2 assembler, as an intiger.
-
-* **Default:** 31
-
-
 GATB Minia Pipeline
 ^^^^^^^^^^^^^^^^^^^
 

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

diff --git a/modules/postprocessing/postprocessing.nf b/modules/postprocessing/postprocessing.nf
@@ -273,10 +273,10 @@ workflow postprocessing_wf {
     PROCESS_SHRIMP_PLOT(phred_csv)
     PLOT_CONTIG_DISTRIBUTION(mapping_df_csv)
     GAP_ASSESSMENT(paf, triple_reference)
-    PLOT_GAP_BOXPLOT(GAP_ASSESSMENT.out.json)
-    PLOT_GAP_REFERENCE(GAP_ASSESSMENT.out.csv)
+    PLOT_GAP_BOXPLOT(GAP_ASSESSMENT.out.json | collect)
+    PLOT_GAP_REFERENCE(GAP_ASSESSMENT.out.csv | collect)
     SNP_ASSESSMENT(paf, triple_reference)
-    PLOT_SNP_REFERENCE(SNP_ASSESSMENT.out.csv)
+    PLOT_SNP_REFERENCE(SNP_ASSESSMENT.out.csv | collect)
     MISASSEMBLY(paf)
     PROCESS_MISASSEMBLY(MISASSEMBLY.out.trace_pkl | collect, MISASSEMBLY.out.contig_length_pkl | collect, MISASSEMBLY.out.misassembly_json | collect, MISASSEMBLY.out.misassembled_reference_json | collect)
     PLOT_MISASSEMBLY(MISASSEMBLY.out.csv | collect)

diff --git a/templates/process_assembly_stats_global.py b/templates/process_assembly_stats_global.py
@@ -36,7 +36,7 @@
     ASSEMBLY_STATS_GLOBAL_FILE = '$assembly_stats_global_files'.split()
     ASSEMBLY_STATS_GLOBAL_FILE_JSON = "$json_report".split()
     N_TARGET = float("$params.n_target")
-    ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "BCALM2": json.loads("$params.bcalm"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"), 
+    ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"), 
                        "MetaHipMer2": json.loads("$params.metahipmer2"), "MINIA": json.loads("$params.minia"), "MEGAHIT": json.loads("$params.megahit"), 
                        "metaSPAdes": json.loads("$params.metaspades"), "Unicycler": json.loads("$params.unicycler"), "SPAdes": json.loads("$params.spades"),
                        "SKESA": json.loads("$params.skesa"), "VelvetOptimiser": json.loads("$params.velvetoptimiser"), "IDBA-UD": json.loads("$params.idba")}

diff --git a/templates/process_assembly_stats_mapping.py b/templates/process_assembly_stats_mapping.py
@@ -33,7 +33,7 @@
 
 if __file__.endswith(".command.sh"):
     ASSEMBLY_STATS_GLOBAL_FILE_JSON = "$json_report".split()
-    ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "BCALM2": json.loads("$params.bcalm"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"), 
+    ASSEMBLER_SKIP = {"ABySS":json.loads("$params.abyss"), "GATBMiniaPipeline": json.loads("$params.gatb_minia"), 
                        "MetaHipMer2": json.loads("$params.metahipmer2"), "MINIA": json.loads("$params.minia"), "MEGAHIT": json.loads("$params.megahit"), 
                        "metaSPAdes": json.loads("$params.metaspades"), "Unicycler": json.loads("$params.unicycler"), "SPAdes": json.loads("$params.spades"),
                        "SKESA": json.loads("$params.skesa"), "VelvetOptimiser": json.loads("$params.velvetoptimiser"), "IDBA-UD": json.loads("$params.idba")}

diff --git a/templates/process_versions.py b/templates/process_versions.py
@@ -37,7 +37,6 @@
 
 ASSEMBLER_PROCESS_DICT = {
     "ABySS": "ABYSS",
-    "BCALM2": "BCALM2",
     "GATBMiniaPipeline": "GATBMINIAPIPELINE",
     "MetaHipMer2": "METAHIPMER2",
     "MINIA": "MINIA",

diff --git a/templates/utils.py b/templates/utils.py
@@ -14,10 +14,10 @@
 COLOURS = ['#a6cee3', '#1f78b4', '#b2df8a', '#33a02c', '#fb9a99', '#e31a1c',
            '#fdbf6f', '#ff7f00', '#cab2d6', '#6a3d9a', '#ebdb75', '#b15928']
 
-ASSEMBLER_NAMES = ["ABySS", "BCALM2", "GATBMiniaPipeline", "MetaHipMer2", "MINIA", "MEGAHIT", "metaSPAdes", "Unicycler", "SPAdes",
+ASSEMBLER_NAMES = ["ABySS", "GATBMiniaPipeline", "MetaHipMer2", "MINIA", "MEGAHIT", "metaSPAdes", "Unicycler", "SPAdes",
                    "SKESA", "VelvetOptimiser", "IDBA-UD"]
 
-ASSEMBLER_PROCESS_LIST = ["ABYSS", "BCALM2", "GATBMINIAPIPELINE", "MINIA", "METAHIPMER2", "MEGAHIT", "METASPADES", "UNICYCLER", "SPADES",
+ASSEMBLER_PROCESS_LIST = ["ABYSS", "GATBMINIAPIPELINE", "MINIA", "METAHIPMER2", "MEGAHIT", "METASPADES", "UNICYCLER", "SPADES",
                           "SKESA", "VELVETOPTIMISER", "IDBA"]