feat: bowtie2 can now sort with samtools and picard

bio/bowtie2/align/environment.linux-64.pin.txt

@@ -1,46 +1,89 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: linux-64
+# created-by: conda 24.9.2
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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bio/bowtie2/align/environment.yaml

@@ -4,5 +4,6 @@ channels:
   - nodefaults
 dependencies:
   - bowtie2 =2.5.4
+  - picard-slim =3.3.0
   - samtools =1.21
   - snakemake-wrapper-utils =0.6.2

bio/bowtie2/align/meta.yaml

@@ -21,5 +21,10 @@ output:
 params:
   - extra: additional program arguments (except for `-x`, `-U`, `-1`, `-2`, `--interleaved`, `-b`, `--met-file`, `--un`, `--al`, `--un-conc`, `--al-conc`, `-f`, `--tab6`, `--tab5`, `-q`, or `-p/--threads`)
   - interleaved: Input `sample` contains interleaved paired-end FASTQ/FASTA reads. `False`(default) or `True`.
+  - sort_program: program to sort the output. `none`(default), `samtools`, or `picard`.
+  - sort_extra: additional arguments for samtools or picard when sorting.
+  - sort_order: choose between `coordinate`(default) or `queryname`.
 notes: |
+  * The `extra` param allows for additional arguments for bowtie2.
+  * The `sort` param allows to enable sorting, and can be either 'none', 'samtools' or 'picard'.
   * This wrapper uses an inner pipe. Make sure to use at least two threads in your Snakefile.

bio/bowtie2/align/test/Snakefile

@@ -101,3 +101,44 @@ rule test_bowtie2_cram:
     threads: 8  # Use at least two threads
     wrapper:
         "master/bio/bowtie2/align"
+
+
+for order in ["coordinate", "queryname"]:
+    for extension in ["sam", "bam", "cram"]:
+        for program in ["none", "samtools", "picard"]:
+
+            rule:
+                name:
+                    f"bowtie2_align_{program}_{order}_{extension}"
+                input:
+                    sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
+                    idx=multiext(
+                        "index/genome",
+                        ".1.bt2",
+                        ".2.bt2",
+                        ".3.bt2",
+                        ".4.bt2",
+                        ".rev.1.bt2",
+                        ".rev.2.bt2",
+                    ),
+                    ref="genome.fasta",
+                output:
+                    f"mapped_idx/{{sample}}.{program}_{order}.{extension}",
+                    # idx="",
+                    # metrics="",
+                    # unaligned="",
+                    # unpaired="",
+                    # unconcordant="",
+                    # concordant="",
+                params:
+                    sort_program=program,
+                    sort_order=order,
+                    sort_extra="",
+                    extra="",
+                log:
+                    f"logs/bowtie2/{{sample}}.{program}_{order}_{extension}.log",
+                params:
+                    extra="",  # optional parameters
+                threads: 8  # Use at least two threads
+                wrapper:
+                    "master/bio/bowtie2/align"