Release 3.1.0

CHANGELOG.md

@@ -3,6 +3,34 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 3.1.0 [2024-10-02]
+
+### `Added`
+
+- [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133)
+
+### `Changed`
+
+- [#664](https://github.com/nf-core/mag/pull/664) - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
+- [#676](https://github.com/nf-core/mag/pull/676) - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133)
+
+### `Fixed`
+
+- [#667](https://github.com/nf-core/mag/pull/667) - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Re-add missing GTDBTk parameters into GTDBTk module (reported by harper357, fixed by @jfy133)
+- [#672](https://github.com/nf-core/mag/pull/673) - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133)
+
+### `Dependencies`
+
+| Tool   | Previous version | New version |
+| ------ | ---------------- | ----------- |
+| GTDBTk | 2.3.2            | 2.4.0       |
+
+### `Deprecated`
+
+- [#670](https://github.com/nf-core/mag/pull/670) - Deprecated --gtdbtk_pplacer_scratch due to unintuitive usage (reported by harper357, fixed by @jfy133)
+
 ## 3.0.3 [2024-08-27]
 
 ### `Added`

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.0.3" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.1.0" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/3.0.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/3.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

bin/summary_gtdbtk.py

@@ -76,11 +76,11 @@ def main(args=None):
     columns = [
         "user_genome",
         "classification",
-        "fastani_reference",
-        "fastani_reference_radius",
-        "fastani_taxonomy",
-        "fastani_ani",
-        "fastani_af",
+        "closest_genome_reference",
+        "closest_genome_reference_radius",
+        "closest_genome_taxonomy",
+        "closest_genome_ani",
+        "closest_genome_af",
         "closest_placement_reference",
         "closest_placement_radius",
         "closest_placement_taxonomy",

conf/base.config

@@ -123,30 +123,30 @@ process {
         cpus          = { check_megahit_cpus (8, task.attempt  ) }
         memory        = { check_max (40.GB * task.attempt, 'memory' ) }
         time          = { check_max (16.h  * task.attempt, 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,104,134,139,250] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 250) ? 'retry' : 'finish' }
     }
     //SPAdes returns error(1) if it runs out of memory (and for other reasons as well...)!
     //exponential increase of memory and time with attempts, keep number of threads to enable reproducibility
     withName: SPADES {
         cpus          = { check_spades_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 21 + 12 + 1) ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     withName: SPADESHYBRID {
         cpus          = { check_spadeshybrid_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 21 + 12 + 1) ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     //returns exit code 247 when running out of memory
     withName: BOWTIE2_ASSEMBLY_ALIGN {
         cpus          = { check_max (2    * task.attempt, 'cpus'   ) }
         memory        = { check_max (8.GB * task.attempt, 'memory' ) }
         time          = { check_max (8.h  * task.attempt, 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 247) ? 'retry' : 'finish' }
     }
     withName: METABAT2_METABAT2 {
         cpus   = { check_max (8     * task.attempt, 'cpus'   ) }
@@ -168,6 +168,6 @@ process {
 
     withName: DASTOOL_DASTOOL {
         // if SCGs not found, bins cannot be assigned and DAS_tool will die with exit status 1
-        errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
     }
 }