diff --git a/seqnado/workflow/rules/fastq_trim.smk b/seqnado/workflow/rules/fastq_trim.smk
index 0fe26c21..a445cfb1 100644
--- a/seqnado/workflow/rules/fastq_trim.smk
+++ b/seqnado/workflow/rules/fastq_trim.smk
@@ -1,9 +1,48 @@
 import seqnado.utils
 
+
+def get_linked_fastq_files(wc):
+    outdir = checkpoints.link_fastqs.get(**wc).output[0]
+    fq_files = list(pathlib.Path(outdir).glob(f"{wc['sample']}*.fastq.gz"))
+    return fq_files
+
+
+checkpoint link_fastqs:
+    input:
+        fastqs=DESIGN.fastq_paths,
+    output:
+        directory("seqnado_output/fastqs"),
+    run:
+        for assay_name, assay in DESIGN.assays.items():
+            if assay.r2:
+                r1_path_new = pathlib.Path(
+                    f"seqnado_output/fastqs/{assay_name}_1.fastq.gz"
+                )
+                r2_path_new = pathlib.Path(
+                    f"seqnado_output/fastqs/{assay_name}_2.fastq.gz"
+                )
+                r1_path_new.symlink_to(assay.r1)
+                r2_path_new.symlink_to(assay.r2)
+            else:
+                r1_path_new = pathlib.Path(
+                    f"seqnado_output/fastqs/{assay_name}.fastq.gz"
+                )
+                r1_path_new.symlink_to(assay.r1)
+
+
+rule confirm_fastqs_renamed:
+    input:
+        fastqs=get_linked_fastq_files,
+    output:
+        touch("seqnado_output/fastqs/.sentinel"),
+
+
 rule trimgalore_paired:
     # Trim reads using trimgalore
     input:
-        unpack(lambda wc: seqnado.utils.translate_fq_files(wc, samples=FASTQ_SAMPLES, paired=True))
+        fq1="seqnado_output/fastqs/{sample}_1.fastq.gz",
+        fq2="seqnado_output/fastqs/{sample}_2.fastq.gz",
+        renamed_sentinel="seqnado_output/fastqs/.sentinel",
     output:
         trimmed1=temp("seqnado_output/trimmed/{sample}_1.fastq.gz"),
         trimmed2=temp("seqnado_output/trimmed/{sample}_2.fastq.gz"),
@@ -12,8 +51,8 @@ rule trimgalore_paired:
         mem_mb=2000,
         time="02:00:00",
     params:
-        options=seqnado.utils.check_options(config['trim_galore']['options']),
-        trim_dir="seqnado_output/trimmed"
+        options=seqnado.utils.check_options(config["trim_galore"]["options"]),
+        trim_dir="seqnado_output/trimmed",
     log:
         "seqnado_output/logs/trimming/{sample}.log",
     shell:
@@ -22,3 +61,29 @@ rule trimgalore_paired:
         mv {params.trim_dir}/{wildcards.sample}_val_1.fq.gz {output.trimmed1} &&
         mv {params.trim_dir}/{wildcards.sample}_val_2.fq.gz {output.trimmed2}
         """
+
+
+rule trimgalore_single:
+    # Trim reads using trimgalore
+    input:
+        fq="seqnado_output/fastq/{sample}.fastq.gz",
+        renamed_sentinel="seqnado_output/fastqs/.sentinel",
+    output:
+        trimmed=temp("seqnado_output/trimmed/{sample}.fastq.gz"),
+    threads: 4
+    resources:
+        mem_mb=2000,
+        time="02:00:00",
+    params:
+        options=seqnado.utils.check_options(config["trim_galore"]["options"]),
+        trim_dir="seqnado_output/trimmed",
+    log:
+        "seqnado_output/logs/trimming/{sample}.log",
+    shell:
+        """
+        trim_galore --cores {threads} {params.options} --basename {wildcards.sample} --output_dir {params.trim_dir} {input.fq} >> {log} 2>&1 &&
+        mv {params.trim_dir}/{wildcards.sample}_trimmed.fq.gz {output.trimmed}
+        """
+
+
+ruleorder: trimgalore_paired > trimgalore_single