feat: bowtie2 can now sort with samtools and picard

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

@@ -1,46 +1,93 @@
 # 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
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bio/bowtie2/align/environment.yaml

@@ -3,6 +3,7 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - bowtie2 =2.5.4
+  - bowtie2 =2.5
+  - picard-slim =3.3
   - samtools =1.21
-  - snakemake-wrapper-utils =0.6.2
+  - snakemake-wrapper-utils =0.6

bio/bowtie2/align/meta.yaml

@@ -5,6 +5,7 @@ authors:
   - Johannes Köster
   - Filipe G. Vieira
   - Thibault Dayris
+  - Jorge Langa
 input:
   - sample: FASTQ file(s)
   - idx: Bowtie2 indexed reference index
@@ -13,13 +14,17 @@ input:
 output:
   - SAM/BAM/CRAM file. This must be the first output file in the output file list.
   - idx: Optional path to bam index.
-  - metrics: Optional path to metrics file.
-  - unaligned: Optional path to unaligned unpaired reads.
-  - unpaired: Optional path to unpaired reads that aligned at least once.
-  - unconcordant: Optional path to pairs that didn't align concordantly.
-  - concordant: Optional path to pairs that aligned concordantly at least once.
+  # - metrics: Optional path to metrics file.
+  # - unaligned: Optional path to unaligned unpaired reads.
+  # - unpaired: Optional path to unpaired reads that aligned at least once.
+  # - unconcordant: Optional path to pairs that didn't align concordantly.
+  # - concordant: Optional path to pairs that aligned concordantly at least once.
 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.
   * This wrapper uses an inner pipe. Make sure to use at least two threads in your Snakefile.

bio/bowtie2/align/test/Snakefile

@@ -1,4 +1,4 @@
-rule test_bowtie2:
+rule test_bowtie2_sam:
     input:
         sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         idx=multiext(
@@ -10,25 +10,16 @@ rule test_bowtie2:
             ".rev.1.bt2",
             ".rev.2.bt2",
         ),
-        # ref="genome.fasta", #Required for CRAM output
     output:
-        "mapped/{sample}.bam",
-        # idx="",
-        # metrics="",
-        # unaligned="",
-        # unpaired="",
-        # unconcordant="",
-        # concordant="",
+        "mapped_sam/{sample}.sam",
     log:
-        "logs/bowtie2/{sample}.log",
-    params:
-        extra="",  # optional parameters
+        "logs/bowtie2/mapped_sam_{sample}.log",
     threads: 8  # Use at least two threads
     wrapper:
         "master/bio/bowtie2/align"
 
 
-use rule test_bowtie2 as test_bowtie2_se_gz with:
+use rule test_bowtie2_sam as test_bowtie2_se_gz with:
     input:
         sample=["reads/{sample}.1.fastq.gz"],
         idx=multiext(
@@ -42,38 +33,26 @@ use rule test_bowtie2 as test_bowtie2_se_gz with:
         ),
     output:
         "mapped_se_gz/{sample}.bam",
+    log:
+        "logs/bowtie2/mapped_se_gz_{sample}.log",
 
 
-rule test_bowtie2_index:
-    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",
-        ),
+use rule test_bowtie2_sam as test_bowtie2_extra_outputs with:
     output:
-        "mapped_idx/{sample}.bam",
-        idx="mapped_idx/{sample}.bam.bai",
-        metrics="mapped_idx/{sample}.metrics.txt",
-        unaligned="mapped_idx/{sample}.unaligned.sam",
-        unpaired="mapped_idx/{sample}.unpaired.sam",
-        # unconcordant="",
-        # concordant="",
+        "mapped_multi/{sample}.bam",
+        idx="mapped_multi/{sample}.bam.bai",
+        # metrics="mapped_multi/{sample}.metrics.txt",
+        # unaligned=["mapped_multi/{sample}.unaligned.1.fq"],
+        # unpaired="mapped_multi/{sample}.unpaired.fq"],
+        # unconcordant="mapped_multi/{sample}.unconcordant.sam",
+        # concordant="mapped_multi/{sample}.concordant.sam",
     log:
-        "logs/bowtie2/{sample}.log",
+        "logs/bowtie2/mapped_multi_{sample}.log",
     params:
-        extra="",  # optional parameters
-    threads: 8  # Use at least two threads
-    wrapper:
-        "master/bio/bowtie2/align"
+        sort_program="samtools",
 
 
-rule test_bowtie2_cram:
+use rule test_bowtie2_sam as test_bowtie2_cram with:
     input:
         sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
         idx=multiext(
@@ -86,18 +65,26 @@ rule test_bowtie2_cram:
             ".rev.2.bt2",
         ),
         ref="genome.fasta",
+        ref_fai="genome.fasta.fai",
     output:
-        "mapped_idx/{sample}.cram",
-        # idx="",
-        # metrics="",
-        # unaligned="",
-        # unpaired="",
-        # unconcordant="",
-        # concordant="",
+        "mapped_cram/{sample}.cram",
     log:
-        "logs/bowtie2/{sample}.log",
+        "logs/bowtie2/samtools_cram_{sample}.log",
+
+
+use rule test_bowtie2_sam as test_bowtie2_sort_samtools with:
+    output:
+        "mapped_samtools/{sample}.bam",
+    log:
+        "logs/bowtie2/mapped_samtools_{sample}.log",
     params:
-        extra="",  # optional parameters
-    threads: 8  # Use at least two threads
-    wrapper:
-        "master/bio/bowtie2/align"
+        sort_program="samtools"
+
+
+use rule test_bowtie2_sam as test_bowtie2_sort_picard with:
+    output:
+        "mapped_picard/{sample}.bam",
+    log:
+        "logs/bowtie2/mapped_picard_{sample}.log",
+    params:
+        sort_program="picard"

bio/bowtie2/align/test/genome.fasta.fai

@@ -0,0 +1 @@
+Sheila	20	8	20	21