Snakemake target rules may not contain wildcards

Question

I am getting the following error when I run

1. snakemake -j8 ph_final and
2. snakemake -j8 q2r: Building DAG of jobs... WorkflowError: Target rules may not contain wildcards. Please specify concrete files or a rule without wildcards at the command line, or have a rule without wildcards at the very top of your workflow (e.g. the typical "rule all" which just collects all results you want to generate in the end).

I am trying to run the following snakemake file for phonons calculations using qe:

configfile: "config.yml"

rule ph_target:
    input:
        expand("ph/V{volume}/ph.in",
            volume=config["eos"]["volumes"]),
        expand("ph/V{volume}/scf.in",
            volume=config["eos"]["volumes"])

rule ph_in:
    input:
        structure="{workdir}/init.qe",
        template_scf=config["phonon"]["template"]["scf"],
        template_ph=config["phonon"]["template"]["ph"],
        job_sh=config["phonon"]["job_sh"]
    output:
        scf_in="{workdir}/scf.in",
        ph_in="{workdir}/ph.in",
        job_sh="{workdir}/job.sh"
    shell:
        '''
        cat {input.template_scf} > {output.scf_in}
        cat {input.structure} >> {output.scf_in}
        cp {input.template_ph} {output.ph_in}
        cp {input.job_sh} {output.job_sh}
        '''

rule ph_structures:
    input:
        structure="relax/V{volume}/final.qe"
    output:
        structure="ph/V{volume}/init.qe"
    shell:
        '''
        cp {input.structure} {output.structure}
        '''

rule ph_final:
    input:
        scf_out="{workdir}/scf.out",
        ph_out="{workdir}/ph.out"
    output:
        scf_done="{workdir}/scf.out.done",
        ph_done="{workdir}/ph.out.done",
        final="{workdir}/ph.final"
    shell:
        '''
        bash scripts/check-done.sh {input.scf_out}
        bash scripts/check-done.sh {input.ph_out}
        bash scripts/check-ph-final.sh {wildcards.workdir}
        '''

rule q2r:
    input:
        ph_final="{workdir}/ph.final",
        template="templates/q2r.in"
    output:
        input="{workdir}/q2r.in",
        out="{workdir}/q2r.out",
        err="{workdir}/q2r.err",
        done="{workdir}/q2r.out.done",
        fc=expand("{{workdir}}/{prefix}.fc", prefix=config["system"]["prefix"])
    shell:
        '''
        cp {input.template} {output.input}
        bash scripts/q2r.sh {output.input}
        bash scripts/check-done.sh {output.out}
        '''

rule matdyn_qha:
    input:
        ph_final="{workdir}/ph.final",
        template="templates/matdyn-qha.in",
        fc=expand("{{workdir}}/{prefix}.fc", prefix=config["system"]["prefix"]),
        weights="weights/weights.txt"
    output:
        input="{workdir}/matdyn-qha.in",
        out="{workdir}/matdyn-qha.out",
        err="{workdir}/matdyn-qha.err",
        done="{workdir}/matdyn-qha.out.done",
        freq=expand("{{workdir}}/{prefix}.freq", prefix=config["system"]["prefix"]),
        eig=expand("{{workdir}}/{prefix}.eig", prefix=config["system"]["prefix"]),
        vec=expand("{{workdir}}/{prefix}.vec", prefix=config["system"]["prefix"])
    shell:
        '''
        cp {input.template} {output.input}
        echo "`cat {input.weights}`" | wc -l >> {output.input}
        cat {input.weights} >> {output.input}
        bash scripts/matdyn.sh {output.input}
        bash scripts/check-done.sh {output.out}
        '''

rule input01:
    params:
        comment=config["system"]["prefix"]
    input:
        expand("ph/V{volume}/ph.final", volume=config["eos"]["volumes"]),
        expand("ph/V{volume}/ph.out.done", volume=config["eos"]["volumes"]),
        freq=expand("ph/V{volume}/{prefix}.freq", prefix=config["system"]["prefix"], volume=config["eos"]["volumes"]),
        weights="weights/weights.txt"
    output:
        input01="input01"
    shell:
        '''
        python3 scripts/make-input01.py -c {params.comment} {input.freq} > {output.input01}
        echo "" >> {output.input01}
        echo "weights" >> {output.input01}
        cat {input.weights} >> {output.input01}
        '''

rule input01_ordered:
    params:
        prefix=config["system"]["prefix"],
        comment=config["system"]["prefix"]
    input:
        expand("ph/V{volume}/ph.final", volume=config["eos"]["volumes"]),
        expand("ph/V{volume}/ph.out.done", volume=config["eos"]["volumes"]),
        freq=expand("ph/V{volume}/{prefix}.freq", prefix=config["system"]["prefix"], volume=config["eos"]["volumes"]),
        eig=expand("ph/V{volume}/{prefix}.eig", prefix=config["system"]["prefix"], volume=config["eos"]["volumes"]),
        weights="weights/weights.txt"
    output:
        input01="input01.ordered"
    shell:
        '''
        python3 scripts/make-input01.py --sort-by {params.prefix}.eig -c {params.comment} {input.freq} > {output.input01}
        echo "" >> {output.input01}
        echo "weights" >> {output.input01}
        cat {input.weights} >> {output.input01}
        '''

rule weights_target:
    params:
        kpts=expand("{nk1},{nk2},{nk3}",
            nk1=config["phonon"]["matdyn_kpts"][0],
            nk2=config["phonon"]["matdyn_kpts"][1],
            nk3=config["phonon"]["matdyn_kpts"][2],
        )
    input:
        scf=expand("ph/V{volume}/scf.in", volume=config["eos"]["volumes"][0])
    output:
        input="weights/weights.in",
        weights="weights/weights.txt"
    shell:
        '''
        python3 scripts/make-weights-input.py {input.scf} --nk {params.kpts} > {output.input}
        bash scripts/gen_coords2.sh {output.input}
        '''

Answer 1

The way you have set up your rule q2r it has one wildcard {workdir} defined in the output block of your rule:

rule q2r:
    input:
        ph_final="{workdir}/ph.final",
        template="templates/q2r.in"
    output:
        input="{workdir}/q2r.in",
        out="{workdir}/q2r.out",
        err="{workdir}/q2r.err",
        done="{workdir}/q2r.out.done",
        fc=expand("{{workdir}}/{prefix}.fc", prefix=config["system"]["prefix"])
    shell:
        '''
        cp {input.template} {output.input}
        bash scripts/q2r.sh {output.input}
        bash scripts/check-done.sh {output.out}
        '''

You need to provide snakemake with a value for {workdir}, either by specifying a path rather than the rule name, e.g.:

snakemake -j8 some-directory-name/q2r.in

or if {workdir} is not supposed to be a wildcard but rather a parameter/variable, change it to such one in the Snakefile, e.g.

WORKDIR = "some-directory-name"

rule q2r:
    input:
        ph_final=f"{WORKDIR}/ph.final",
        template="templates/q2r.in"
    output:
        input=f"{WORKDIR}/q2r.in",
        out=f"{WORKDIR}/q2r.out",
        err=f"{WORKDIR}/q2r.err",
        done=f"{WORKDIR}/q2r.out.done",
        fc=expand("{workdir}/{prefix}.fc", workdir=WORKDIR, prefix=config["system"]["prefix"])
    shell:
        '''
        cp {input.template} {output.input}
        bash scripts/q2r.sh {output.input}
        bash scripts/check-done.sh {output.out}
        '''