Bump the version before the patch release v.1.2.2

nf-core · Dec 19, 2024 · 9b0e463 · 9b0e463
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commit 9b0e463
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diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/tree/dev" target="_blank">nf-core/taxprofiler</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/taxprofiler/dev/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler/releases/tag/1.2.2"
+  target="_blank">nf-core/taxprofiler</a> analysis pipeline. For information about
+  how to interpret these results, please see the <a href="https://nf-co.re/taxprofiler/1.2.2/docs/output"
+  target="_blank">documentation</a>.
 report_section_order:
   "nf-core-taxprofiler-methods-description":
     order: -1000
@@ -60,23 +61,23 @@ custom_logo_url: https://nf-co.re/taxprofiler
 custom_logo_title: "nf-core/taxprofiler"
 
 run_modules:
-  - fastqc
-  - adapterremoval
-  - fastp
-  - nonpareil
-  - bbduk
-  - prinseqplusplus
-  - porechop
-  - filtlong
-  - nanoq
-  - bowtie2
-  - samtools
-  - kraken
-  - kaiju
-  - diamond
-  - malt
-  - motus
-  - custom_content
+- fastqc
+- adapterremoval
+- fastp
+- nonpareil
+- bbduk
+- prinseqplusplus
+- porechop
+- filtlong
+- nanoq
+- bowtie2
+- samtools
+- kraken
+- kaiju
+- diamond
+- malt
+- motus
+- custom_content
 
 sp:
   diamond:
@@ -92,67 +93,81 @@ sp:
     contents_re: " "
 
 top_modules:
-  - "fastqc":
-      name: "FastQC / Falco (pre-Trimming)"
-      path_filters:
-        - "*raw*"
-      path_filters_exclude:
-        - "*processed*"
-      extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
-  - "fastqc":
-      name: "FastQC / Falco (post-Trimming)"
-      path_filters:
-        - "*processed*"
-      path_filters_exclude:
-        - "*raw*"
-      extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
-  - nonpareil
-  - "porechop":
-      name: "Porechop"
-      anchor: "porechop"
-      target: "Porechop"
-      path_filters:
-        - "*porechop.log"
-      extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated."
-  - "porechop":
-      name: "Porechop_ABI"
-      anchor: "porechop_abi"
-      target: "Porechop_ABI"
-      doi: "10.1093/bioadv/vbac085"
-      info: "find and remove adapters from Oxford Nanopore reads."
-      path_filters:
-        - "*porechop_abi.log"
-      extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop_abi did not detect any adapters and therefore no statistics generated."
-  - "bowtie2":
-      name: "bowtie2"
-  - "samtools":
-      name: "Samtools Stats"
-  - "kraken":
-      name: "Kraken"
-      path_filters:
-        - "*.kraken2.kraken2.report.txt"
-  - "kraken":
-      name: "Bracken"
-      anchor: "bracken"
-      target: "Bracken"
-      doi: "10.7717/peerj-cs.104"
-      info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
-      extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC."
-      path_filters:
-        - "*.bracken.kraken2.report.txt"
-  - "kraken":
-      name: "Centrifuge"
-      anchor: "centrifuge"
-      target: "Centrifuge"
-      doi: "10.1101/gr.210641.116"
-      info: "is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. Note: Figure title"
-      extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
-      path_filters:
-        - "*.centrifuge.txt"
-  - "malt":
-      name: "MALT"
-  - "kaiju":
-      name: "Kaiju"
+- "fastqc":
+    name: "FastQC / Falco (pre-Trimming)"
+    path_filters:
+    - "*raw*"
+    path_filters_exclude:
+    - "*processed*"
+    extra: "If used in this run, Falco is a drop-in replacement for FastQC producing
+      the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
+- "fastqc":
+    name: "FastQC / Falco (post-Trimming)"
+    path_filters:
+    - "*processed*"
+    path_filters_exclude:
+    - "*raw*"
+    extra: "If used in this run, Falco is a drop-in replacement for FastQC producing
+      the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
+- nonpareil
+- "porechop":
+    name: "Porechop"
+    anchor: "porechop"
+    target: "Porechop"
+    path_filters:
+    - "*porechop.log"
+    extra: "ℹ️: if you get the error message 'Error - was not able to plot data.'
+      this means that porechop did not detect any adapters and therefore no statistics
+      generated."
+- "porechop":
+    name: "Porechop_ABI"
+    anchor: "porechop_abi"
+    target: "Porechop_ABI"
+    doi: "10.1093/bioadv/vbac085"
+    info: "find and remove adapters from Oxford Nanopore reads."
+    path_filters:
+    - "*porechop_abi.log"
+    extra: "ℹ️: if you get the error message 'Error - was not able to plot data.'
+      this means that porechop_abi did not detect any adapters and therefore no statistics
+      generated."
+- "bowtie2":
+    name: "bowtie2"
+- "samtools":
+    name: "Samtools Stats"
+- "kraken":
+    name: "Kraken"
+    path_filters:
+    - "*.kraken2.kraken2.report.txt"
+- "kraken":
+    name: "Bracken"
+    anchor: "bracken"
+    target: "Bracken"
+    doi: "10.7717/peerj-cs.104"
+    info: "Estimates species abundances in metagenomics samples by probabilistically
+      re-distributing reads in the taxonomic tree."
+    extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing
+      the same output format as Kraken. Abundance information is currently not supported
+      in MultiQC."
+    path_filters:
+    - "*.bracken.kraken2.report.txt"
+- "kraken":
+    name: "Centrifuge"
+    anchor: "centrifuge"
+    target: "Centrifuge"
+    doi: "10.1101/gr.210641.116"
+    info: "is a very rapid and memory-efficient system for the classification of DNA
+      sequences from microbial samples. The system uses a novel indexing scheme based
+      on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index.
+      Note: Figure title"
+    extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output
+      format as Kraken. If activated, see the actual Kraken2 results in the section
+      above."
+    path_filters:
+    - "*.centrifuge.txt"
+- "malt":
+    name: "MALT"
+- "kaiju":
+    name: "Kaiju"
 
 # It is not possible to set placement for custom kraken
 # and centrifuge columns.
@@ -264,81 +279,81 @@ table_columns_placement:
 
 table_columns_visible:
   FastQC / Falco (pre-Trimming):
-    total_sequences: True
-    avg_sequence_length: True
-    percent_duplicates: True
-    percent_gc: True
-    percent_fails: False
+    total_sequences: true
+    avg_sequence_length: true
+    percent_duplicates: true
+    percent_gc: true
+    percent_fails: false
   FastQC / Falco (post-Trimming):
-    total_sequences: True
-    avg_sequence_length: True
-    percent_duplicates: False
-    percent_gc: False
-    percent_fails: False
+    total_sequences: true
+    avg_sequence_length: true
+    percent_duplicates: false
+    percent_gc: false
+    percent_fails: false
   Adapter Removal:
-    aligned_total: True
-    percent_aligned: True
-    percent_collapsed: True
-    percent_discarded: False
+    aligned_total: true
+    percent_aligned: true
+    percent_collapsed: true
+    percent_discarded: false
   fastp:
-    pct_adapter: True
-    pct_surviving: True
-    pct_duplication: False
-    after_filtering_gc_content: False
-    after_filtering_q30_rate: False
-    after_filtering_q30_bases: False
+    pct_adapter: true
+    pct_surviving: true
+    pct_duplication: false
+    after_filtering_gc_content: false
+    after_filtering_q30_rate: false
+    after_filtering_q30_bases: false
   nonpareil:
     nonpareil_R: false
     nonpareil_LR: false
     nonpareil_kappa: true
     nonpareil_C: true
     nonpareil_diversity: true
   porechop:
-    Input reads: False
+    Input reads: false
     Start Trimmed:
-    Start Trimmed Percent: True
-    End Trimmed: False
-    End Trimmed Percent: True
-    Middle Split: False
-    Middle Split Percent: True
+    Start Trimmed Percent: true
+    End Trimmed: false
+    End Trimmed Percent: true
+    Middle Split: false
+    Middle Split Percent: true
   porechop_abi:
-    Input reads: False
+    Input reads: false
     Start Trimmed:
-    Start Trimmed Percent: True
-    End Trimmed: False
-    End Trimmed Percent: True
-    Middle Split: False
-    Middle Split Percent: True
+    Start Trimmed Percent: true
+    End Trimmed: false
+    End Trimmed Percent: true
+    Middle Split: false
+    Middle Split Percent: true
   Filtlong:
-    Target bases: True
+    Target bases: true
   nanoq:
-    ReadN50: True
-    Reads: True
+    ReadN50: true
+    Reads: true
   BBDuk:
-    Input reads: False
-    Total Removed bases Percent: False
-    Total Removed bases: False
-    Total Removed reads percent: True
-    Total Removed reads: False
+    Input reads: false
+    Total Removed bases Percent: false
+    Total Removed bases: false
+    Total Removed reads percent: true
+    Total Removed reads: false
   "PRINSEQ++":
-    prinseqplusplus_total: True
+    prinseqplusplus_total: true
   bowtie2:
-    overall_alignment_rate: True
+    overall_alignment_rate: true
   Samtools Stats:
-    raw_total_sequences: True
-    reads_mapped: True
-    reads_mapped_percent: True
-    reads_properly_paired_percent: False
-    non-primary_alignments: False
-    reads_MQ0_percent: False
-    error_rate: False
-  Kraken: False
-  Bracken: False
-  Centrifuge: False
-  DIAMOND: False
-  Kaiju: False
-  MALT: False
-  motus: False
+    raw_total_sequences: true
+    reads_mapped: true
+    reads_mapped_percent: true
+    reads_properly_paired_percent: false
+    non-primary_alignments: false
+    reads_MQ0_percent: false
+    error_rate: false
+  Kraken: false
+  Bracken: false
+  Centrifuge: false
+  DIAMOND: false
+  Kaiju: false
+  MALT: false
+  motus: false
 
 table_columns_name:
   FastQC / Falco (pre-Trimming):
@@ -359,18 +374,19 @@ table_columns_name:
     reads_mapped_percent: "% Mapped Reads"
 
 extra_fn_clean_exts:
-  - "kraken2.report.txt"
-  - ".txt"
-  - ".settings"
-  - ".bbduk"
-  - ".unmapped"
-  - "_filtered"
-  - "porechop"
-  - "porechop_abi"
-  - "_processed"
-  - ".diamond"
-  - type: remove
-    pattern: "_falco"
+- "kraken2.report.txt"
+- ".txt"
+- ".settings"
+- ".bbduk"
+- ".unmapped"
+- "_filtered"
+- "porechop"
+- "porechop_abi"
+- "_processed"
+- ".diamond"
+- type: remove
+  pattern: "_falco"
 
 section_comments:
-  general_stats: "By default, all read count columns are displayed as millions (M) of reads."
+  general_stats: "By default, all read count columns are displayed as millions (M)
+    of reads."
diff --git a/nextflow.config b/nextflow.config
@@ -420,7 +420,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.3.0.dev'
+    version         = '1.2.2'
     doi             = '10.1101/2023.10.20.563221'
 }